Thread: [Apbs-users] database of PQR files
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From: Xevi B. F. <xbi...@si...> - 2008-09-26 12:33:23
|
Hi all, did anybody set-up a database of PQR files? (specially for ligands it maybe tedious for non experts to set-up a proper PQR file) a college of mine is looking for a PQR file for the FAD cofactor (FlavonAdeninDinucleotide). Could anyone share this PQR file? thank you! Xevi. |
From: Nathan B. <nat...@ma...> - 2008-09-26 13:13:33
|
Hello -- > did anybody set-up a database of PQR files? > > (specially for ligands it maybe tedious for non experts to set-up a > proper PQR file) We've discussed this possibility in the past. However, there are so many options available with PDB2PQR it seemed unlikely that we'd be able to incorporate enough variation in the PQR setup to make the database useful for a broad range of users. Thanks, Nathan > > a college of mine is looking for a PQR file for the FAD cofactor > (FlavonAdeninDinucleotide). Could anyone share this PQR file? > > thank you! > > > Xevi. > > > > > > > > > ------------------------------------------------------------------------- > 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: Yong Jung<yj...@fs...> - 2008-09-27 13:29:56
|
Hi! Prof. Nathan Baker (Last summer, I met Dr. Andy, Dr. Holst, Dr. Bori, and Dr. Ben at UCSD. I enjoyed having nice weather, good food and talking with nice people. Then I read your papers of computational methods and they were fantastic. So, I would like to ask you a simple question that I could not get its answer during last several weeks.) The main problem: We assume 100 cubic (1 angstrom x 1 angstrom x 1angstrom) boxes lined consisting of z-axis. This 100 boxes have its original electric potentials (like e1, e2, .....e100) acquired from the external environmental electrostatic forces. We assume that two potassium ions (cations with one positive electron charge each) cross along this box lines. Then two K ions stop at position P and Q. The question is that: What is the electric potential at point p (actually a cubic box) ? If a point F (or a cube) is located at a 10th cube, not P and Q where K ions reside, the electric potential at 10 = e10 (original electric potential at a 10th cube) + ke/r1D + ke/r1D where r1 is a distance between F and P, r2 is a distance between F and Q, and D is a dieletric constant. However, if a K ion reside in a point (a cube) P, what is NEW electric potential of P? I guessed: The electric potential at P = eP (original electric potential at a Pth cube) + ke/r3D (r3 is a distance between P and Q) + WHAT(?). (Is WHAT(?) self-electric potential?) If we know that the a positive electron charge is uniformly distributed on the surface of a K ion (its radius is 1.33 angstrom), its electric potential ( WHAT(?)) could be ke/Rd, where R is 1.33 angstrom and d is the dielectric constant inside a K ion). Is it right? Then how do we know d? What's relationship between D and d? Does it make a peak point? or the answer is just ke/r3D (r3 is a distance between P and Q), deleting eP (original electric potential at a Pth cube) + WHAT(?). Who experienced this special situation? With Prof. Nathan, if anybody answer me this complicated question exactly, I will buy your beers later. Thanks. Woon. ----- Original Message ----- From: Nathan Baker <nat...@ma...> Date: Friday, September 26, 2008 9:18 am Subject: Re: [Apbs-users] database of PQR files To: Xevi Biarnes Fontal <xbi...@si...> Cc: apb...@li... > Hello -- > > > did anybody set-up a database of PQR files? > > > > (specially for ligands it maybe tedious for non experts to set- > up a > > proper PQR file) > > We've discussed this possibility in the past. However, there are > so > many options available with PDB2PQR it seemed unlikely that we'd > be > able to incorporate enough variation in the PQR setup to make the > database useful for a broad range of users. > > Thanks, > > Nathan > > > > > a college of mine is looking for a PQR file for the FAD cofactor > > (FlavonAdeninDinucleotide). Could anyone share this PQR file? > > > > thank you! > > > > > > Xevi. > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------- > -------- > > 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/ > > > > > > > ------------------------------------------------------------------- > ------ > This SF.Net email is sponsored by the Moblin Your Move Developer's > challengeBuild 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 > -- Best wishes, Yongwoon Jung ================================== Department of Mathematics Florida State University Tallahassee, FL 32306 Home) 850-893-9848 |
From: Xevi B. (S. <xbi...@si...> - 2008-09-29 10:55:03
|
Thank you for your reply. Assuming a fixed ForceField and a fixed protonation state, what is the variability in PQR file due to? Is it "just" a matter of conformational flexibility of the ligand that may generate a different atomic charge distribution? I know this is not "just" a simple point ;-) is there any other reason? best regards, Xevi -----Mensaje original----- De: Nathan Baker [mailto:nat...@ma...] Enviado el: divendres, 26 / setembre / 2008 15:13 Para: Xevi Biarnes Fontal CC: apb...@li... Asunto: Re: [Apbs-users] database of PQR files Hello -- > did anybody set-up a database of PQR files? > > (specially for ligands it maybe tedious for non experts to set-up a > proper PQR file) We've discussed this possibility in the past. However, there are so many options available with PDB2PQR it seemed unlikely that we'd be able to incorporate enough variation in the PQR setup to make the database useful for a broad range of users. Thanks, Nathan > > a college of mine is looking for a PQR file for the FAD cofactor > (FlavonAdeninDinucleotide). Could anyone share this PQR file? > > thank you! > > > Xevi. > > > > > > > > > ------------------------------------------------------------------------- > 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/ No virus found in this incoming message. Checked by AVG - http://www.avg.com Version: 8.0.169 / Virus Database: 270.7.3/1694 - Release Date: 26/09/2008 18:55 |
From: Yong Jung<yj...@fs...> - 2008-09-27 13:25:26
|
Hi! Prof. Nathan Baker (Last summer, I met Dr. Andy, Dr. Holst, Dr. Bori, and Dr. Ben at UCSD. I enjoyed having nice weather, good food and talking with nice people. Then I read your papers of computational methods and they were fantastic. So, I would like to ask you a simple question that I could not get its answer during last several weeks.) The main problem: We assume 100 cubic (1 angstrom x 1 angstrom x 1angstrom) boxes lined consisting of z-axis. This 100 boxes have its original electric potentials (like e1, e2, .....e100) acquired from the external environmental electrostatic forces. We assume that two potassium ions (cations with one positive electron charge each) cross along this box lines. Then two K ions stop at position P and Q. The question is that: What is the electric potential at point p (actually a cubic box) ? If a point F (or a cube) is located at a 10th cube, not P and Q where K ions reside, the electric potential at 10 = e10 (original electric potential at a 10th cube) + ke/r1D + ke/r1D where r1 is a distance between F and P, r2 is a distance between F and Q, and D is a dieletric constant. However, if a K ion reside in a point (a cube) P, what is NEW electric potential of P? I guessed: The electric potential at P = eP (original electric potential at a Pth cube) + ke/r3D (r3 is a distance between P and Q) + WHAT(?). (Is WHAT(?) self-electric potential?) If we know that the a positive electron charge is uniformly distributed on the surface of a K ion (its radius is 1.33 angstrom), its electric potential ( WHAT(?)) could be ke/Rd, where R is 1.33 angstrom and d is the dielectric constant inside a K ion). Is it right? Then how do we know d? What's relationship between D and d? Does it make a peak point? or the answer is just ke/r3D (r3 is a distance between P and Q), deleting eP (original electric potential at a Pth cube) + WHAT(?). Who experienced this special situation? With Prof. Nathan, if anybody answer me this complicated question exactly, I will buy your beers later. Thanks. W. ----- Original Message ----- From: Nathan Baker <nat...@ma...> Date: Friday, September 26, 2008 9:18 am Subject: Re: [Apbs-users] database of PQR files To: Xevi Biarnes Fontal <xbi...@si...> Cc: apb...@li... > Hello -- > > > did anybody set-up a database of PQR files? > > > > (specially for ligands it maybe tedious for non experts to set- > up a > > proper PQR file) > > We've discussed this possibility in the past. However, there are > so > many options available with PDB2PQR it seemed unlikely that we'd > be > able to incorporate enough variation in the PQR setup to make the > database useful for a broad range of users. > > Thanks, > > Nathan > > > > > a college of mine is looking for a PQR file for the FAD cofactor > > (FlavonAdeninDinucleotide). Could anyone share this PQR file? > > > > thank you! > > > > > > Xevi. > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------- > -------- > > 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/ > > > > > > > ------------------------------------------------------------------- > ------ > This SF.Net email is sponsored by the Moblin Your Move Developer's > challengeBuild 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 > -- Best wishes, Yongwoon Jung ================================== Department of Mathematics Florida State University Tallahassee, FL 32306 Home) 850-893-9848 |
From: Abdullah K. <abd...@eb...> - 2008-09-26 14:01:05
Attachments:
1jr8_ligand0FAD.pqr
|
Try this one. The partial charges are calculated based on the MMFF94 forcefield. The radii are Pauling's van der Waals radii (PARSE uses the same radii). All the best Abdullah |
From: Nathan B. <nat...@ma...> - 2008-09-30 17:20:08
|
Hello -- The complexity is due to the wide range of options provided by PDB2PQR (http://pdb2pqr.sourceforge.net/userguide.html#using) associated with optimization, titration state assignment, and force field choices. You're right: with a fixed titration state and force field this probably wouldn't be too problematic. Starting with PARSE and pH 7.0 would probably be sufficient for many users' needs. Thanks, Nathan On Sep 29, 2008, at 5:54 AM, Xevi Biarnés (SISSA) wrote: > Thank you for your reply. > > Assuming a fixed ForceField and a fixed protonation state, what is the > variability in PQR file due to? Is it "just" a matter of > conformational > flexibility of the ligand that may generate a different atomic charge > distribution? > > I know this is not "just" a simple point ;-) > > is there any other reason? > > best regards, > > > Xevi > > > > > > -----Mensaje original----- > De: Nathan Baker [mailto:nat...@ma...] > Enviado el: divendres, 26 / setembre / 2008 15:13 > Para: Xevi Biarnes Fontal > CC: apb...@li... > Asunto: Re: [Apbs-users] database of PQR files > > Hello -- > >> did anybody set-up a database of PQR files? >> >> (specially for ligands it maybe tedious for non experts to set-up a >> proper PQR file) > > We've discussed this possibility in the past. However, there are so > many options available with PDB2PQR it seemed unlikely that we'd be > able to incorporate enough variation in the PQR setup to make the > database useful for a broad range of users. > > Thanks, > > Nathan > >> >> a college of mine is looking for a PQR file for the FAD cofactor >> (FlavonAdeninDinucleotide). Could anyone share this PQR file? >> >> thank you! >> >> >> Xevi. >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> 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/ > > > > > > > No virus found in this incoming message. > Checked by AVG - http://www.avg.com > Version: 8.0.169 / Virus Database: 270.7.3/1694 - Release Date: > 26/09/2008 > 18:55 > > > ------------------------------------------------------------------------- > 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: Nathan B. <nat...@ma...> - 2008-09-28 21:23:46
|
Hi Yongwoon -- > (Last summer, I met Dr. Andy, Dr. Holst, Dr. Bori, and Dr. Ben at > UCSD. I enjoyed having nice weather, good food and talking with > nice people. Then I read your papers of computational methods and > they were fantastic. So, I would like to ask you a simple question > that I could not get its answer during last several weeks.) Thanks! > The main problem: We assume 100 cubic (1 angstrom x 1 angstrom x > 1angstrom) boxes lined consisting of z-axis. This 100 boxes have > its original electric potentials (like e1, e2, .....e100) acquired > from the external environmental electrostatic forces. We assume > that two potassium ions (cations with one positive electron charge > each) cross along this box lines. Then two K ions stop at position > P and Q. Can you clarify the problem setup? What are the specific dimensions of the system? The way you've stated the problem seems to imply that you're interested in a system with a x-length of 1 Å a y-length of 1 Å and a z-length of 100 Å. Is this correct? What are the cubes for? Do they represent the discretization of the problem and/or the discretization of the applied potentials? What are the boundary conditions? > The question is that: What is the electric potential at point p > (actually a cubic box) ? > If a point F (or a cube) is located at a 10th cube, not P and Q > where K ions reside, > the electric potential at 10 = e10 (original electric potential at > a 10th cube) + ke/r1D + ke/r1D > where r1 is a distance between F and P, r2 is a distance between F > and Q, and D is a dieletric constant. Are there any dielectric boundaries in the system or other reasons why simple superposition wouldn't apply? > However, if a K ion reside in a point (a cube) P, what is NEW > electric potential of P? > I guessed: The electric potential at P = eP (original electric > potential at a Pth cube) > + ke/r3D (r3 is a distance between P and Q) + WHAT(?). (Is WHAT(?) > self-electric potential?) I'm not sure because I don't know the answers to the questions above. > If we know that the a positive electron charge is uniformly > distributed on the surface of a K ion (its radius is > 1.33 angstrom), its electric potential ( WHAT(?)) could be ke/Rd, > where R is 1.33 angstrom and d is the dielectric constant inside a K > ion). Is it right? Then how do we know d? What's relationship > between D and d? Does it make a peak point? or the answer is > just ke/r3D (r3 is a distance between P and Q), > deleting eP (original electric potential at a Pth cube) + WHAT(?). > Who experienced this special situation? I think we need to know more about (1) the boundary conditions and (2) the dielectric profile before an answer can be given. Thanks, Nathan > With Prof. Nathan, if anybody answer me this complicated question > exactly, I will buy your beers later. > > Thanks. W. > > ----- Original Message ----- > From: Nathan Baker <nat...@ma...> > Date: Friday, September 26, 2008 9:18 am > Subject: Re: [Apbs-users] database of PQR files > To: Xevi Biarnes Fontal <xbi...@si...> > Cc: apb...@li... > >> Hello -- >> >>> did anybody set-up a database of PQR files? >>> >>> (specially for ligands it maybe tedious for non experts to set- >> up a >>> proper PQR file) >> >> We've discussed this possibility in the past. However, there are >> so >> many options available with PDB2PQR it seemed unlikely that we'd >> be >> able to incorporate enough variation in the PQR setup to make the >> database useful for a broad range of users. >> >> Thanks, >> >> Nathan >> >>> >>> a college of mine is looking for a PQR file for the FAD cofactor >>> (FlavonAdeninDinucleotide). Could anyone share this PQR file? >>> >>> thank you! >>> >>> >>> Xevi. >>> >>> >>> >>> >>> >>> >>> >>> >>> ----------------------------------------------------------------- >> -------- >>> 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/ >> >> >> >> >> >> >> ------------------------------------------------------------------- >> ------ >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challengeBuild 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 >> > > -- > Best wishes, > > Yongwoon Jung > ================================== > Department of Mathematics > Florida State University > Tallahassee, FL 32306 > Home) 850-893-9848 -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Yong Jung<yj...@fs...> - 2008-09-29 01:24:38
|
Hi! Prof. Nathan and everythbody. I realized that my question was not proper one in this APBS family. Since PB and PNP solver has some problems in treating narrow ion channels, I invented Atomistic to Continuum model. In a single file ion sytem, we only care the electric potential the route that ions cross. Then we can find work and net current, whatever. Using Poisson solver (excluding ion flow), we can get internal electric potential of pore. If one line is enough and channel length is 100 angstrom, we can extract the electric potentials from one line-100 cubic boxes. Then we place discrete ions at the cental line ( one line-100 cubic boxes). Then we get other new electric potentials of one line-100 cubic boxes calculated from a few discrete ions. The question is: If a K ion (radius 1.33 A) resides in a small box (or a point in 1-D), how can we calculate the electric potential at that box? The neighboring boxes should have high electric potential due to a resident K ion. Then the point (or box) that the K ion stands should have electric potential equal to larger than the neighboring boxes (common sense!). We think water molecules are inside the channel (dielectric constant = 60 or 70/80). This morning, I made an AtC model and solved this problem. Since we don't care the electric potential inside a K ion because it itself does not contribute (attract or destroy) to its outside electric field, now the answer is to find out the electric potential of the nearest point. In the K ion case, the nearest integer point is the distance of 2 angstrom far away. If we find it, we can assume it is the approximate electric potential of the box (or the point) where a K ion stands, I guess. Here, we have another problem. The point (2 angstrom far awy) means that it locates 0.67 angstrom from the surface of a K ion. In calculating its electric potential caused by a K ion (formula, ke/rD, where D is dielectric constnat of this area), we can't apply D=60 or 70/80 because this blending area (mixed zone of discrete ion atomistic model and water continuum model). In this area, we should make a possible model to find the proper dielectric constant. So, I got an answer, but I don't know how much it is reliable. This is my idea. If you have other idea, please let me know. I am afraid that others do not understand what I am talking about. The continuum model can't isolate the self-energy (the internal energy that a K ion has) and has a big problem in narrow ion channel cases. So, this problem was asked. I wish you will have a good luck in this fall. Now, everybody can forget this problem from now on if you are not really interested in this question. P.S. If I need your help more, I will send you an email to describe the problem in detail. ----- Original Message ----- From: Nathan Baker <nat...@ma...> Date: Sunday, September 28, 2008 5:23 pm Subject: Re: [Apbs-users] Asking an atomistic model problem (Coulomb Law) To: yj...@fs... Cc: Xevi Biarnes Fontal <xbi...@si...>, apb...@li... > Hi Yongwoon -- > > > (Last summer, I met Dr. Andy, Dr. Holst, Dr. Bori, and Dr. Ben > at > > UCSD. I enjoyed having nice weather, good food and talking > with > > nice people. Then I read your papers of computational methods > and > > they were fantastic. So, I would like to ask you a simple > question > > that I could not get its answer during last several weeks.) > > Thanks! > > > The main problem: We assume 100 cubic (1 angstrom x 1 angstrom > x > > 1angstrom) boxes lined consisting of z-axis. This 100 boxes > have > > its original electric potentials (like e1, e2, .....e100) > acquired > > from the external environmental electrostatic forces. We assume > > > that two potassium ions (cations with one positive electron > charge > > each) cross along this box lines. Then two K ions stop at > position > > P and Q. > > Can you clarify the problem setup? What are the specific > dimensions > of the system? The way you've stated the problem seems to imply > that > you're interested in a system with a x-length of 1 Å a y-length of > 1 Å > and a z-length of 100 Å. Is this correct? > > What are the cubes for? Do they represent the discretization of > the > problem and/or the discretization of the applied potentials? > > What are the boundary conditions? > > > The question is that: What is the electric potential at point > p > > (actually a cubic box) ? > > If a point F (or a cube) is located at a 10th cube, not P and Q > > where K ions reside, > > the electric potential at 10 = e10 (original electric potential > at > > a 10th cube) + ke/r1D + ke/r1D > > where r1 is a distance between F and P, r2 is a distance > between F > > and Q, and D is a dieletric constant. > > Are there any dielectric boundaries in the system or other reasons > why > simple superposition wouldn't apply? > > > However, if a K ion reside in a point (a cube) P, what is NEW > > electric potential of P? > > I guessed: The electric potential at P = eP (original electric > > > potential at a Pth cube) > > + ke/r3D (r3 is a distance between P and Q) + WHAT(?). (Is > WHAT(?) > > self-electric potential?) > > I'm not sure because I don't know the answers to the questions above. > > > If we know that the a positive electron charge is uniformly > > distributed on the surface of a K ion (its radius is > > 1.33 angstrom), its electric potential ( WHAT(?)) could be > ke/Rd, > > where R is 1.33 angstrom and d is the dielectric constant inside > a K > > ion). Is it right? Then how do we know d? What's > relationship > > between D and d? Does it make a peak point? or the answer is > > > just ke/r3D (r3 is a distance between P and Q), > > deleting eP (original electric potential at a Pth cube) + > WHAT(?). > > Who experienced this special situation? > > I think we need to know more about (1) the boundary conditions and > (2) > the dielectric profile before an answer can be given. > > Thanks, > > Nathan > > > With Prof. Nathan, if anybody answer me this complicated > question > > exactly, I will buy your beers later. > > > > Thanks. W. > > > > ----- Original Message ----- > > From: Nathan Baker <nat...@ma...> > > Date: Friday, September 26, 2008 9:18 am > > Subject: Re: [Apbs-users] database of PQR files > > To: Xevi Biarnes Fontal <xbi...@si...> > > Cc: apb...@li... > > > >> Hello -- > >> > >>> did anybody set-up a database of PQR files? > >>> > >>> (specially for ligands it maybe tedious for non experts to set- > >> up a > >>> proper PQR file) > >> > >> We've discussed this possibility in the past. However, there are > >> so > >> many options available with PDB2PQR it seemed unlikely that we'd > >> be > >> able to incorporate enough variation in the PQR setup to make the > >> database useful for a broad range of users. > >> > >> Thanks, > >> > >> Nathan > >> > >>> > >>> a college of mine is looking for a PQR file for the FAD cofactor > >>> (FlavonAdeninDinucleotide). Could anyone share this PQR file? > >>> > >>> thank you! > >>> > >>> > >>> Xevi. > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> --------------------------------------------------------------- > -- > >> -------- > >>> 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/ > >> > >> > >> > >> > >> > >> > >> ---------------------------------------------------------------- > --- > >> ------ > >> This SF.Net email is sponsored by the Moblin Your Move Developer's > >> challengeBuild 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 > >> > > > > -- > > Best wishes, > > > > Yongwoon Jung > > ================================== > > Department of Mathematics > > Florida State University > > Tallahassee, FL 32306 > > Home) 850-893-9848 > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > > > > -- Best wishes, Yongwoon Jung ================================== Department of Mathematics Florida State University Tallahassee, FL 32306 Home) 850-893-9848 |