Thread: [Apbs-users] atom # is off the mesh (ignoring) ERROR
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From: Pinar K. <pin...@gm...> - 2008-11-20 16:11:29
|
Hi All, i am trying to calculate the solvation energy for protein complex that consists of protein1.pqr + protein2.pqr (they combine into 0.pqr) I am getting the following error for my unbound components : Vpmg_fillco: Atom #2283 at (-41.216, 18.857, 37.138) is off the mesh (ignoring): Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 Vpmg_fillco: zmin = -4.33315, zmax = 106.998 Vpmg_fillco: Atom #2284 at (-40.036, 19.940, 38.625) is off the mesh (ignoring): Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 Vpmg_fillco: zmin = -4.33315, zmax = 106.998 Vpmg_fillco: Atom #2285 at (-39.403, 19.044, 38.811) is off the mesh (ignoring): Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 Vpmg_fillco: zmin = -4.33315, zmax = 106.998 . . . I wonder if there is something wrong with my input file? I center all the grids on molecule 1 (0.pqr) . But when i center grid on molecule2 for molecule2 and molecule3 for molecule3 this error does not occur. Do you have any comment about the reasons of my problem? Below is my .in file: read mol pqr 0.pqr mol pqr 0_protein1.pqr mol pqr 0_protein2.pqr end elec name complex1 mg-auto dime 161 129 161 cglen 103.0795 98.5847 111.3313 fglen 80.6350 77.9910 85.4890 *cgcent* mol 1 *fgcent* mol 1 mol 1 lpbe bcfl sdh pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name pro1 mg-auto dime 161 129 161 cglen 103.0795 98.5847 111.3313 fglen 80.6350 77.9910 85.4890 *cgcent* mol* 1* *fgcent* mol *1* mol 2 lpbe bcfl sdh pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name pro2 mg-auto dime 161 129 161 cglen 103.0795 98.5847 111.3313 fglen 80.6350 77.9910 85.4890 *cgcent *mol *1* * fgcent* mol *1* mol 3 lpbe bcfl sdh pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end print elecEnergy complex1 - pro1 - pro2 end quit Thanks in advance Pinar Kanlikilicer Bogazici University /Chemical Engineering Graduate Student Istanbul/ TURKIYE |
From: Gernot K. <ge...@ch...> - 2008-11-20 17:30:08
|
Hi! On Thu, 2008-11-20 at 18:11 +0200, Pinar KANLIKILICER wrote: > I wonder if there is something wrong with my input file? I center all > the grids on molecule 1 (0.pqr) . But when i center grid on molecule2 > for molecule2 and molecule3 for molecule3 this error does not occur. > Do you have any comment about the reasons of my problem? Looks like the position of the center of geometry is different for the molecules in 0_protein1.pqr and 0_protein2.pqr than for the individual monomers in 0.pqr. You could try again preparing alternative protein1/2 files by copy & pasting from 0.pqr. Your input file seems to look fine. Greetings, Gernot |
From: Nathan B. <ba...@bi...> - 2008-11-20 22:41:47
|
Hello -- Which of the molecules in your input file is the complex? Are the coordinates for the components of the complex the same in all PDB files (i.e., a rigid body problem)? If so, you should probably be centering all calculations on the complex PDB. Thanks, Nathan On Nov 20, 2008, at 10:11 AM, Pinar KANLIKILICER wrote: > Hi All, > i am trying to calculate the solvation energy for protein complex > that consists of protein1.pqr + protein2.pqr (they combine into > 0.pqr) > > I am getting the following error for my unbound components : > > Vpmg_fillco: Atom #2283 at (-41.216, 18.857, 37.138) is off the > mesh (ignoring): > Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 > Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 > Vpmg_fillco: zmin = -4.33315, zmax = 106.998 > Vpmg_fillco: Atom #2284 at (-40.036, 19.940, 38.625) is off the > mesh (ignoring): > Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 > Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 > Vpmg_fillco: zmin = -4.33315, zmax = 106.998 > Vpmg_fillco: Atom #2285 at (-39.403, 19.044, 38.811) is off the > mesh (ignoring): > Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 > Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 > Vpmg_fillco: zmin = -4.33315, zmax = 106.998 > . > . > . > > > > I wonder if there is something wrong with my input file? I center > all the grids on molecule 1 (0.pqr) . But when i center grid on > molecule2 for molecule2 and molecule3 for molecule3 this error does > not occur. Do you have any comment about the reasons of my problem? > > Below is my .in file: > > read > mol pqr 0.pqr > mol pqr 0_protein1.pqr > mol pqr 0_protein2.pqr > end > elec name complex1 > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > cgcent mol 1 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > end > elec name pro1 > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > cgcent mol 1 > fgcent mol 1 > mol 2 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > > end > elec name pro2 > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > cgcent mol 1 > fgcent mol 1 > mol 3 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > end > > print elecEnergy complex1 - pro1 - pro2 end > quit > > > Thanks in advance > > > Pinar Kanlikilicer > Bogazici University /Chemical Engineering Graduate Student > Istanbul/ TURKIYE > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Pinar K. <pin...@gm...> - 2008-11-21 10:02:47
|
0.pqr is the complex (molecule1). I constructed these files according to the results of molecular dynamic simulations. PDB files (which were used in pdb2pqr web server) are the snaphots which were extracted from MD simulations belonging to protein1,protein2 and complex simulations,separately. So coordinates are not the same in all PDB files. for example: protein1's pdb file is like that: ATOM 1 N HSD A 26 2.810 1.396 10.088 1.00 0.00 ATOM 2 HT1 HSD A 26 1.828 1.235 10.186 1.00 0.00 ATOM 3 HT2 HSD A 26 3.114 2.072 10.760 1.00 0.00 ATOM 4 HT3 HSD A 26 3.310 0.539 10.216 1.00 0.00 ATOM 5 CA HSD A 26 3.076 1.906 8.748 1.00 0.00 . . and complex pdb file which begins with protein1 is like that: ATOM 1 N HSD A 26 1.916 9.763 68.811 1.00 0.00 ATOM 2 HT1 HSD A 26 1.231 10.379 69.201 1.00 0.00 ATOM 3 HT2 HSD A 26 2.141 10.049 67.880 1.00 0.00 ATOM 4 HT3 HSD A 26 2.740 9.767 69.378 1.00 0.00 ATOM 5 CA HSD A 26 1.359 8.377 68.773 1.00 0.00 2008/11/20 Nathan Baker <ba...@bi...> Hello -- > Which of the molecules in your input file is the complex? Are the > coordinates for the components of the complex the same in all PDB files > (i.e., a rigid body problem)? If so, you should probably be centering all > calculations on the complex PDB. > > Thanks, > > Nathan > > > On Nov 20, 2008, at 10:11 AM, Pinar KANLIKILICER wrote: > > Hi All, > i am trying to calculate the solvation energy for protein complex that > consists of protein1.pqr + protein2.pqr (they combine into > 0.pqr) > > I am getting the following error for my unbound components : > > Vpmg_fillco: Atom #2283 at (-41.216, 18.857, 37.138) is off the mesh > (ignoring): > Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 > Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 > Vpmg_fillco: zmin = -4.33315, zmax = 106.998 > Vpmg_fillco: Atom #2284 at (-40.036, 19.940, 38.625) is off the mesh > (ignoring): > Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 > Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 > Vpmg_fillco: zmin = -4.33315, zmax = 106.998 > Vpmg_fillco: Atom #2285 at (-39.403, 19.044, 38.811) is off the mesh > (ignoring): > Vpmg_fillco: xmin = -36.1202, xmax = 66.9592 > Vpmg_fillco: ymin = -22.2223, ymax = 76.3623 > Vpmg_fillco: zmin = -4.33315, zmax = 106.998 > . > . > . > > > > I wonder if there is something wrong with my input file? I center all the > grids on molecule 1 (0.pqr) . But when i center grid on molecule2 for > molecule2 and molecule3 for molecule3 this error does not occur. Do you have > any comment about the reasons of my problem? > > Below is my .in file: > > read > mol pqr 0.pqr > mol pqr 0_protein1.pqr > mol pqr 0_protein2.pqr > end > elec name complex1 > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > *cgcent* mol 1 > *fgcent* mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > end > elec name pro1 > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > *cgcent* mol* 1* > *fgcent* mol *1* > mol 2 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > > end > elec name pro2 > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > *cgcent *mol *1* > * fgcent* mol *1* > mol 3 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > end > > print elecEnergy complex1 - pro1 - pro2 end > quit > > > Thanks in advance > > > Pinar Kanlikilicer > Bogazici University /Chemical Engineering Graduate Student > Istanbul/ TURKIYE > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > > > > > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > > > > -- ٩(͡๏̯͡๏)۶ pinar |
From: Gernot K. <ge...@ch...> - 2008-11-21 11:25:49
|
Hi! On Fri, 2008-11-21 at 12:02 +0200, Pinar KANLIKILICER wrote: > > 0.pqr is the complex (molecule1). I constructed these files according > to the results of molecular dynamic simulations. PDB files (which were > used in pdb2pqr web server) are the snaphots which were extracted from > MD simulations belonging to protein1,protein2 and complex > simulations,separately. So coordinates are not the same in all PDB > files. So just before you generate PQR files, just run the Kabsch algorithm on your snapshots from the monomer MD, i.e. align the monomor coordinates on the dimer structure. Greetings, Gernot |
From: Nathan B. <ba...@bi...> - 2008-11-21 12:25:30
|
Hi Pinar -- Gernot is right; these molecules need to be aligned. However, in order to use the electrostatic energy calculation method you're describing, these molecules need to be *perfectly* aligned since you're relying on this alignment to cancel self-interaction energies. Please be sure to check that the atoms are in the same locations after alignment. Thanks, Nathan On Fri, Nov 21, 2008 at 6:25 AM, Gernot Kieseritzky < ge...@ch...> wrote: > Hi! > > On Fri, 2008-11-21 at 12:02 +0200, Pinar KANLIKILICER wrote: > > > > 0.pqr is the complex (molecule1). I constructed these files according > > to the results of molecular dynamic simulations. PDB files (which were > > used in pdb2pqr web server) are the snaphots which were extracted from > > MD simulations belonging to protein1,protein2 and complex > > simulations,separately. So coordinates are not the same in all PDB > > files. > > So just before you generate PQR files, just run the Kabsch algorithm on > your snapshots from the monomer MD, i.e. align the monomor coordinates > on the dimer structure. > > Greetings, > Gernot > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Gernot K. <ge...@ch...> - 2008-11-21 13:26:43
|
Hi! > these molecules need to be *perfectly* aligned since you're relying on > this alignment to cancel self-interaction energies. Please be sure to > check that the atoms are in the same locations after alignment. Yes, I forgot the self-energy. Perfect alignment by rigid-body alignment is not possible in her case since the subunits will adopt slightly different conformations in the monomer case compared to the dimer situation. So, Pinar, what you should do to compute the association energy for the protein complex (I guess, this is what you ultimately want to achieve) is to compute the total electrostatic energy for the dimer ( E(d) ) and the monomers ( E(m1), E(m2) ) individually and then compute the difference E(d) - ( E(m1) + E(m2) ) How to compute the total dielectric energy? E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x, homogenious) ^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ use 'coulomb.c' in the APBS with pdie!=sdie APBS with pdie=sdie APBS distribution with and no ions eps = pdie The difference E(x, inh) - E(x,hom) will ensure that the grid artifact cancels. To compare with possible experimental values in case of protein-protein association you will also need to include the non-electrostatic contribution to the solvation energy and add this to E(x). Greetings, Gernot |
From: Pinar K. <pin...@gm...> - 2008-11-25 14:17:06
|
Thank you for your replies. I am calculating electrostatic energies individually. But one thing about input files confused me. Should i use directly the input files which pdb2pqr gave me or should i omit second part which has the value of 2.00 for the dielectric value of the solvent (*sdie*). Because, input files are usually constructed based on the value of 78.4 for dielectric coefficient of the solvent? pdb2pqr result : read mol pqr 0.pqr end elec mg-auto dime 161 129 161 cglen 103.0795 98.5847 111.3313 fglen 80.6350 77.9910 85.4890 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl sdh pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no write pot dx pot end *elec mg-auto dime 161 129 161 cglen 103.0795 98.5847 111.3313 fglen 80.6350 77.9910 85.4890 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl sdh pdie 2.0000 sdie 2.0000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end* print elecEnergy 2 - 1 end quit 2008/11/21 Gernot Kieseritzky <ge...@ch...> > Hi! > > > these molecules need to be *perfectly* aligned since you're relying on > > this alignment to cancel self-interaction energies. Please be sure to > > check that the atoms are in the same locations after alignment. > > Yes, I forgot the self-energy. Perfect alignment by rigid-body alignment > is not possible in her case since the subunits will adopt slightly > different conformations in the monomer case compared to the dimer > situation. > > So, Pinar, what you should do to compute the association energy for the > protein complex (I guess, this is what you ultimately want to achieve) > is to compute the total electrostatic energy for the dimer ( E(d) ) and > the monomers ( E(m1), E(m2) ) individually and then compute the > difference > > E(d) - ( E(m1) + E(m2) ) > > How to compute the total dielectric energy? > > E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x, homogenious) > ^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ > use 'coulomb.c' in the APBS with pdie!=sdie APBS with pdie=sdie > APBS distribution with and no ions > eps = pdie > > The difference E(x, inh) - E(x,hom) will ensure that the grid artifact > cancels. > > To compare with possible experimental values in case of protein-protein > association you will also need to include the non-electrostatic > contribution to the solvation energy and add this to E(x). > > Greetings, > Gernot > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- ٩(͡๏̯͡๏)۶ pinar |
From: Nathan B. <ba...@bi...> - 2008-11-25 16:30:32
|
Hello -- If you are just using the systems with the inhomogeneous dielectric to calculate the binding energy (e.g., in the rigid body type of binding problem that I described in an earlier e-mail), then the homogeneous calculations with both sdie and pdie set to 2.00 are unnecessary. If, on the other hand, you're calculating binding energies by combining changes in solvation and Coulombic energies, then these calculations are an integral part of your overall calculation. -- Nathan On Tue, Nov 25, 2008 at 8:17 AM, Pinar KANLIKILICER <pin...@gm...>wrote: > Thank you for your replies. > I am calculating electrostatic energies individually. But one thing about > input files confused me. Should i use directly the input files which pdb2pqr > gave me or should i omit second part which has the value of 2.00 for the > dielectric value of the solvent (*sdie*). Because, input files are usually > constructed based on the value of 78.4 for dielectric coefficient of the > solvent? > > pdb2pqr result : > > read > mol pqr 0.pqr > end > elec > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > cgcent mol 1 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > write pot dx pot > end > *elec > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > cgcent mol 1 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 2.0000 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > end > * > print elecEnergy 2 - 1 end > quit > > > 2008/11/21 Gernot Kieseritzky <ge...@ch...> > > Hi! >> >> > these molecules need to be *perfectly* aligned since you're relying on >> > this alignment to cancel self-interaction energies. Please be sure to >> > check that the atoms are in the same locations after alignment. >> >> Yes, I forgot the self-energy. Perfect alignment by rigid-body alignment >> is not possible in her case since the subunits will adopt slightly >> different conformations in the monomer case compared to the dimer >> situation. >> >> So, Pinar, what you should do to compute the association energy for the >> protein complex (I guess, this is what you ultimately want to achieve) >> is to compute the total electrostatic energy for the dimer ( E(d) ) and >> the monomers ( E(m1), E(m2) ) individually and then compute the >> difference >> >> E(d) - ( E(m1) + E(m2) ) >> >> How to compute the total dielectric energy? >> >> E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x, homogenious) >> ^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ >> use 'coulomb.c' in the APBS with pdie!=sdie APBS with pdie=sdie >> APBS distribution with and no ions >> eps = pdie >> >> The difference E(x, inh) - E(x,hom) will ensure that the grid artifact >> cancels. >> >> To compare with possible experimental values in case of protein-protein >> association you will also need to include the non-electrostatic >> contribution to the solvation energy and add this to E(x). >> >> Greetings, >> Gernot >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users >> > > > > -- > ٩(͡๏̯͡๏)۶ pinar > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Changrong Ge <cha...@db...> - 2008-11-25 14:49:08
|
Hi everyone, I am a new guy to this APBS application, in my case I want to calculate electrostatic potentials also. but there is some problems with several pdb files of my database. some I could get , but the other I could not, for example for "2GEJ", there is a problem with this. after runing APBS there is always a popup saying "unable to assign parameters for the 151 atoms in selection unassigned-------". Did anyone meet this problem? how to solve this problem? Need you help. Thanks so much. /Changrong Date: Tue, 25 Nov 2008 16:17:02 +0200From: pin...@gm...To: ge...@ch...CC: apb...@li...Subject: Re: [Apbs-users] atom # is off the mesh (ignoring) ERRORThank you for your replies.I am calculating electrostatic energies individually. But one thing about input files confused me. Should i use directly the input files which pdb2pqr gave me or should i omit second part which has the value of 2.00 for the dielectric value of the solvent (sdie). Because, input files are usually constructed based on the value of 78.4 for dielectric coefficient of the solvent?pdb2pqr result :read mol pqr 0.pqrendelec mg-auto dime 161 129 161 cglen 103.0795 98.5847 111.3313 fglen 80.6350 77.9910 85.4890 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl sdh pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no write pot dx potendelec mg-auto dime 161 129 161 cglen 103.0795 98.5847 111.3313 fglen 80.6350 77.9910 85.4890 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl sdh pdie 2.0000 sdie 2.0000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce noendprint elecEnergy 2 - 1 endquit 2008/11/21 Gernot Kieseritzky <ge...@ch...> Hi! > these molecules need to be *perfectly* aligned since you're relying on> this alignment to cancel self-interaction energies. Please be sure to> check that the atoms are in the same locations after alignment.Yes, I forgot the self-energy. Perfect alignment by rigid-body alignmentis not possible in her case since the subunits will adopt slightlydifferent conformations in the monomer case compared to the dimersituation.So, Pinar, what you should do to compute the association energy for theprotein complex (I guess, this is what you ultimately want to achieve)is to compute the total electrostatic energy for the dimer ( E(d) ) andthe monomers ( E(m1), E(m2) ) individually and then compute thedifferenceE(d) - ( E(m1) + E(m2) )How to compute the total dielectric energy?E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x, homogenious) ^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ use 'coulomb.c' in the APBS with pdie!=sdie APBS with pdie=sdie APBS distribution with and no ions eps = pdieThe difference E(x, inh) - E(x,hom) will ensure that the grid artifactcancels.To compare with possible experimental values in case of protein-proteinassociation you will also need to include the non-electrostaticcontribution to the solvation energy and add this to E(x).Greetings,Gernot -------------------------------------------------------------------------This SF.Net email is sponsored by the Moblin Your Move Developer's challengeBuild the coolest Linux based applications with Moblin SDK & win great prizesGrand prize is a trip for two to an Open Source event anywhere in the worldhttp://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________apbs-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/apbs-users-- ٩(͡๏̯͡๏)۶ pinar _________________________________________________________________ Get more done, have more fun, and stay more connected with Windows Mobile®. http://clk.atdmt.com/MRT/go/119642556/direct/01/ |
From: Nathan B. <ba...@bi...> - 2008-11-26 22:35:23
|
Hello -- How are you running APBS? Through PyMOL? Are you assigning parameters with PDB2PQR (http://pdb2pqr.sf.net/)? Thanks, Nathan On Tue, Nov 25, 2008 at 8:48 AM, Changrong Ge <cha...@db...> wrote: > Hi everyone, > I am a new guy to this APBS application, in my case I want to calculate > electrostatic potentials also. but there is some problems with several pdb > files of my database. some I could get , but the other I could not, for > example for "2GEJ", there is a problem with this. after runing APBS there is > always a popup saying "unable to assign parameters for the 151 atoms in > selection unassigned-------". Did anyone meet this problem? how to solve > this problem? Need you help. > Thanks so much. > /Changrong > > > ------------------------------ > > Date: Tue, 25 Nov 2008 16:17:02 +0200 > From: pin...@gm... > To: ge...@ch... > CC: apb...@li... > Subject: Re: [Apbs-users] atom # is off the mesh (ignoring) ERROR > > > Thank you for your replies. > I am calculating electrostatic energies individually. But one thing about > input files confused me. Should i use directly the input files which pdb2pqr > gave me or should i omit second part which has the value of 2.00 for the > dielectric value of the solvent (*sdie*). Because, input files are usually > constructed based on the value of 78.4 for dielectric coefficient of the > solvent? > > pdb2pqr result : > > read > mol pqr 0.pqr > end > elec > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > cgcent mol 1 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > write pot dx pot > end > *elec > mg-auto > dime 161 129 161 > cglen 103.0795 98.5847 111.3313 > fglen 80.6350 77.9910 85.4890 > cgcent mol 1 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 2.0000 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > end* > print elecEnergy 2 - 1 end > quit > > > > 2008/11/21 Gernot Kieseritzky <ge...@ch...> > > Hi! > > > these molecules need to be *perfectly* aligned since you're relying on > > this alignment to cancel self-interaction energies. Please be sure to > > check that the atoms are in the same locations after alignment. > > Yes, I forgot the self-energy. Perfect alignment by rigid-body alignment > is not possible in her case since the subunits will adopt slightly > different conformations in the monomer case compared to the dimer > situation. > > So, Pinar, what you should do to compute the association energy for the > protein complex (I guess, this is what you ultimately want to achieve) > is to compute the total electrostatic energy for the dimer ( E(d) ) and > the monomers ( E(m1), E(m2) ) individually and then compute the > difference > > E(d) - ( E(m1) + E(m2) ) > > How to compute the total dielectric energy? > > E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x, homogenious) > ^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ > use 'coulomb.c' in the APBS with pdie!=sdie APBS with pdie=sdie > APBS distribution with and no ions > eps = pdie > > The difference E(x, inh) - E(x,hom) will ensure that the grid artifact > cancels. > > To compare with possible experimental values in case of protein-protein > association you will also need to include the non-electrostatic > contribution to the solvation energy and add this to E(x). > > Greetings, > Gernot > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > -- > ٩(͡๏̯͡๏)۶ pinar > > ------------------------------ > Get more done, have more fun, and stay more connected with Windows Mobile(R). > See how. <http://clk.atdmt.com/MRT/go/119642556/direct/01/> > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Pinar K. <pin...@gm...> - 2010-07-15 12:28:46
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Hi, We are trying to calculate the interaction energy for a protein - protein complex and used apbs to calculate the PB energy. While analyzing our result, we were confused and had the following questions: 1. The input file that we use is the following: read mol pqr protein.pqr end elec mg-auto dime 161 193 161 cglen 102.8602 121.8832 96.3985 fglen 80.5060 91.6960 76.7050 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl sdh pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no write pot dx pot end elec mg-auto dime 161 193 161 cglen 102.8602 121.8832 96.3985 fglen 80.5060 91.6960 76.7050 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl sdh pdie 2.0000 sdie 2.0000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end print elecEnergy 2 - 1 end quit The resulting apbs energy is a positive value. Is this because the way the input file works is Ehomogenious -Einhomogenious? If so, do we need to multiply the resulting value by -1? 2. In our MD simulations, we used a dielectric constant of 1. However, the dielectric constant used in the above input file is 2. Should we change pdie to 1? If so, will we need to change sdie to 1 to get the homogenous part of the apbs energy? Thank you very much Pinar. 2008/11/21 Gernot Kieseritzky <ge...@ch...> > Hi! > > > these molecules need to be *perfectly* aligned since you're relying on > > this alignment to cancel self-interaction energies. Please be sure to > > check that the atoms are in the same locations after alignment. > > Yes, I forgot the self-energy. Perfect alignment by rigid-body alignment > is not possible in her case since the subunits will adopt slightly > different conformations in the monomer case compared to the dimer > situation. > > So, Pinar, what you should do to compute the association energy for the > protein complex (I guess, this is what you ultimately want to achieve) > is to compute the total electrostatic energy for the dimer ( E(d) ) and > the monomers ( E(m1), E(m2) ) individually and then compute the > difference > > E(d) - ( E(m1) + E(m2) ) > > How to compute the total dielectric energy? > > E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x, homogenious) > ^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ > use 'coulomb.c' in the APBS with pdie!=sdie APBS with pdie=sdie > APBS distribution with and no ions > eps = pdie > > The difference E(x, inh) - E(x,hom) will ensure that the grid artifact > cancels. > > To compare with possible experimental values in case of protein-protein > association you will also need to include the non-electrostatic > contribution to the solvation energy and add this to E(x). > > Greetings, > Gernot > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- pinar |
From: Gernot K. <ge...@ch...> - 2010-07-15 13:19:59
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Hi! On Thu, 2010-07-15 at 15:18 +0300, Pinar KANLIKILICER wrote: > Hi, > > We are trying to calculate the interaction energy for a protein - > protein complex and used apbs to calculate the PB energy. While > analyzing our result, we were confused and had the following > questions: > > 1. The input file that we use is the following: > > The resulting apbs energy is a positive value. Is this because the way > the input file works is Ehomogenious -Einhomogenious? If so, do we > need to multiply the resulting value by -1? Yes, because what you do here is to compute a solvation energy obtained upon transferring the protein from a vacuum characterized by \epsilon=2 into the solvent which turns into an inhomogenious medium once the protein is solvated. > 2. In our MD simulations, we used a dielectric constant of 1. However, > the dielectric constant used in the above input file is 2. Should we > change pdie to 1? If so, will we need to change sdie to 1 to get the > homogenous part of the apbs energy? Actually, I would even suggest to consider setting pdie to a value of 4 if it gives better results. I would not worry too much about the dielectric constant being different in case of MD since MD and PBE are two completely different ball games. The MD force field is simply parameterized assuming pdie=1. But you are using MD simply as a source of physically reasonable conformations (I guess because it looks like what you're doing is an MM/PBSA approach). What the correct choice of pdie is in a PBE computation, is a long and complicated story. The physical interpretation of pdie is the protein medium's inherent capability of polarizing in response to a charge. If the protein is like an organic solvent pdie=2 is ok, since this is the value you obtain typically for apolar solvents from the Clausius–Mossotti relation. It is due to the electronic polarizabilty of the molecule. A higher value would suggest the protein is more polar than an apolar organic solvent which is a reasonable assumption because polar protein groups are not completely fixed and can reorient in response to an electric field. However, no precise value can be given since every protein is different. Typical values, however, are 4, 8 or 20. We always use 4 for pKA and redox computations because this value usually gave reasonable results in the past and we stick to it also for consistency. One could, however, also think of pdie as a free parameter that can be used to tune the results. If you can compare with known experimental values you just set pdie to a value which gives the best agreement. As long as the dielectric constant is not far outside the usual interval between 2 and 20, that is acceptable. Check also "What are the dielectric constants of proteins and how to validate electrostatic models?" by Claudia N. Schutz and Arieh Warshel: http://dx.doi.org/10.1002/prot.1106 Best regards, Gernot Kieseritzky |