Thread: Re: [Apbs-users] (no subject) (Page 2)
Biomolecular electrostatics software
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From: Thomas J. <jue...@gm...> - 2007-12-18 09:21:05
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If you don't want to receive anymore mails, unsubscribe from the APBS-users list. You can do this by going to https://lists.sourceforge.net/lists/listinfo/apbs-users and entering your email at: "To unsubscribe from apbs-users, get a password reminder, or change your subscription options enter your subscription email address:" Cheers, Thomas On Dec 18, 2007 1:08 AM, silvia speroni <sil...@gm...> wrote: > please stop sending me these e-mails, I've already solved my problem with > APBS. > Thanks > > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services > for just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > |
From: Palmier, M. O. (MU-Student) <mo...@mi...> - 2008-09-04 14:09:46
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Hello, I'm trying to use APBS to produce a solvated surface map of my protein. I get errors that point to the histidines in the pqr input file. The original pdb file is fine. When I look at the file I see that all of the histidines in the protein have zeros in the two far right columns. Atoms from all other residues are fine. What should I edit into these zero values? Regards, Mark Mark O. Palmier, MS mo...@mi... Biochemistry Department, 117 Schweitzer Hall University of Missouri, Columbia, MO 65211 phone: (573) 884-6405; FAX: (573) 884-4812 |
From: Nathan B. <nat...@ma...> - 2008-09-04 15:47:09
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Hello -- How did you generate this file with the problematic histidines? Thanks, Nathan On Sep 4, 2008, at 9:09 AM, Palmier, Mark Oliver (MU-Student) wrote: > Hello, > > I’m trying to use APBS to produce a solvated surface map of my > protein. I get errors that point to the histidines in the pqr input > file. The original pdb file is fine. When I look at the file I see > that all of the histidines in the protein have zeros in the two far > right columns. Atoms from all other residues are fine. What should > I edit into these zero values? > > Regards, > Mark > > Mark O. Palmier, MS > mo...@mi... > Biochemistry Department, 117 Schweitzer Hall > University of Missouri, Columbia, MO 65211 > phone: (573) 884-6405; FAX: (573) 884-4812 > > ------------------------------------------------------------------------- > 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: <lap...@du...> - 2009-05-06 05:22:13
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please remove me from this email list |
From: Fernando Z. <fer...@gm...> - 2009-09-08 14:46:22
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Hi! I am trying to generate a .pqr file from a cellular membrane .pdb file with the pdb2pqr server. It seems that the server will not be able to do it. Is there another way to do it? Thanks! Fernando. -- Bioq. Fernando Zamarreño Grupo de Biofísica Dpto. de Física Univerisdad Nacional del Sur Avda. Alem 1253 - (8000) Bahia Blanca Tel.: +54 (291) 4595101 Ext 2805 Fax:+54 (291) 4595142 http://www.uns.edu.ar ------------------------------------------------------- |
From: Yong H. <yhu...@gm...> - 2009-09-08 15:10:20
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Hello, Could you send us an example with your pdb file in it, so that we can determine the true nature of this issue? Thanks, Yong 2009/9/8 Fernando Zamarreño <fer...@gm...> > Hi! > I am trying to generate a .pqr file from a cellular membrane .pdb file with > the pdb2pqr server. It seems that the server will not be able to do it. Is > there another way to do it? > Thanks! > Fernando. > > > -- > > Bioq. Fernando Zamarreño > Grupo de Biofísica > Dpto. de Física > Univerisdad Nacional del Sur > Avda. Alem 1253 - (8000) Bahia Blanca > > Tel.: +54 (291) 4595101 Ext 2805 > Fax:+54 (291) 4595142 > http://www.uns.edu.ar > ------------------------------------------------------- > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Yong Huang, D.Sc. Center for Computational Biology Washington University School of Medicine |
From: Yong H. <yhu...@gm...> - 2009-09-08 15:32:52
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Hello, Sorry but it looks like there are no amino acids or nucleic acids in your pdb, as a result, PDB2PQR will be unable to perform its designed routines: adding limited number of missing heavy atoms, placing missing hydrogens, optimizing hydrogen-bond network, debumping atoms, assigning charge and radius parameters from different forcefields, etc. In this case, PDB2PQR will not be very useful to your analysis. Sorry, Yong 2009/9/8 Fernando Zamarreño <fer...@gm...> > Perhaps the file is too heavy?? > > 2009/9/8 Yong Huang <yhu...@gm...> > > Hello, >> >> Could you send us an example with your pdb file in it, so that we can >> determine the true nature of this issue? >> >> Thanks, >> >> Yong >> >> >> 2009/9/8 Fernando Zamarreño <fer...@gm...> >> >>> Hi! >>> I am trying to generate a .pqr file from a cellular membrane .pdb file >>> with the pdb2pqr server. It seems that the server will not be able to do it. >>> Is there another way to do it? >>> Thanks! >>> Fernando. >>> >>> >>> -- >>> >>> Bioq. Fernando Zamarreño >>> Grupo de Biofísica >>> Dpto. de Física >>> Univerisdad Nacional del Sur >>> Avda. Alem 1253 - (8000) Bahia Blanca >>> >>> Tel.: +54 (291) 4595101 Ext 2805 >>> Fax:+54 (291) 4595142 >>> http://www.uns.edu.ar >>> ------------------------------------------------------- >>> >>> >>> ------------------------------------------------------------------------------ >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>> 30-Day >>> trial. Simplify your report design, integration and deployment - and >>> focus on >>> what you do best, core application coding. Discover what's new with >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> _______________________________________________ >>> apbs-users mailing list >>> apb...@li... >>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>> >>> >> >> >> -- >> Yong Huang, D.Sc. >> >> Center for Computational Biology >> Washington University School of Medicine >> > > > > -- > > Bioq. Fernando Zamarreño > Grupo de Biofísica > Dpto. de Física > Univerisdad Nacional del Sur > Avda. Alem 1253 - (8000) Bahia Blanca > > Tel.: +54 (291) 4595101 Ext 2805 > Fax:+54 (291) 4595142 > http://www.uns.edu.ar > ------------------------------------------------------- > -- Yong Huang, D.Sc. Center for Computational Biology Washington University School of Medicine |
From: Mitra K. <mit...@ya...> - 2010-07-15 08:23:50
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From: Nathan A. B. <ba...@ch...> - 2003-08-20 13:06:32
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Hi Frank -- >1) I have been doing calculations on a group of small organic molecules >(less than 40 atoms). I have been advised to use either a 1.4 A or 0.0 A >solvent radius (srad). Does anyone know which to use? This is anyone's guess -- I'd choose the surface definition that gives you the best agreement with experiment. Recent work by HX Zhou would suggest this should be the van der Waals (srad 0.0) surface. >2) When setting the grid lengths, how much should the grid extend beyound >the borders of the molecule? I usually choose either 1.5 * (radius of bounding sphere of molecule) or some multiple of the Debye/Bjerrum length (i.e. 7-10 A). >3) Lastly, after calculating the electrostatic contribution to the total >free energy of solvation via APBS, I am now trying to determine the short >range contributions to this energu. Does anyone know of any APBS output >that may assist me in determining any of the parameters (surface tensions, >molecular areas) necessary to calculate this term(s)? The program apbs/tools/acc should do the trick. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc |
From: DV <die...@md...> - 2004-01-15 22:54:38
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Hi Nathan, checking the examples, in particular PKA-LIG, I noticed that by varying the srad parameter from 1.4 to 0.0 the electrostatic Delta Energy dE changes in about an order of magnitude... same thing happens in UHBD (as the files read) and APBS. srad=0.0 (VdW) | srad=1.4 (molec) +----------------------------------- APBS | 6.6465 | 97.0147 kJ/mol UHBD | 8.876 | 86.50 kJ/mol This figures are obtained by doing dE=E(AB)-E(A)-E(B) as the *in file says. The shift (between the two runs) is tipically of 0.5 % of any value. E(AB) is of order 1E+5 kJ/mol, and dE < 1E2 kJ/mol. So this would mean that none of the digits is valid in the above calculations? (unless we have other source of info so we can know in advance the right value for srad... Could that be the work of HX Zhou? do you have the reference?) Isn´t this a big issue in these calculations? Saludos Diego -----Mensaje original----- De: apb...@ch... [mailto:apb...@ch...]En nombre de Nathan A. Baker Enviado el: Miércoles, 20 de Agosto de 2003 08:07 a.m. Para: Frank D Ducheneaux CC: APBS Users Hi Frank -- >1) I have been doing calculations on a group of small organic molecules >(less than 40 atoms). I have been advised to use either a 1.4 A or 0.0 A >solvent radius (srad). Does anyone know which to use? This is anyone's guess -- I'd choose the surface definition that gives you the best agreement with experiment. Recent work by HX Zhou would suggest this should be the van der Waals (srad 0.0) surface. |
From: Nathan B. <ba...@bi...> - 2004-01-17 05:49:38
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Yes, this is exactly the behavior described by Zhou; I think the best reference is http://www.biophysj.org/cgi/content/abstract/83/3/1341. They make the conclusion that any any behavior predicted by PB theory should be robust with respect to the surface definition chosen. Clearly, however, there are quantiative differences between the different models. Therefore, I'd add that the results depend strongly on the parameters (particularly radii) and that these parameters should be chosen in manner consistent with the surface definition. This is clear from your results below and also pointed out in various PB parameterization papers (see one by Nina & Roux cited in the APBS manual). Thanks, Nathan -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc > -----Original Message----- > From: apb...@ch... > [mailto:apb...@ch...] On Behalf Of DV > Sent: Thursday, January 15, 2004 2:54 AM > To: APBS Users > Subject: RE: [Apbs-users] SRAD > > > Hi Nathan, > > checking the examples, in particular PKA-LIG, I noticed that > by varying the srad parameter from 1.4 to 0.0 the > electrostatic Delta Energy dE changes in about an order of > magnitude... same thing happens in UHBD (as the files > read) and APBS. > > srad=0.0 (VdW) | srad=1.4 (molec) > +----------------------------------- > APBS | 6.6465 | 97.0147 kJ/mol > UHBD | 8.876 | 86.50 kJ/mol > > This figures are obtained by doing dE=E(AB)-E(A)-E(B) as the > *in file says. The shift (between the two runs) is tipically > of 0.5 % of any value. > E(AB) is of order 1E+5 kJ/mol, and dE < 1E2 kJ/mol. So this > would mean that none of the digits is valid in the above > calculations? (unless we have other source of info so we can > know in advance the right value for srad... Could that be the > work of HX Zhou? do you have the reference?) Isn´t this a big > issue in these calculations? > > > Saludos > Diego > > -----Mensaje original----- > De: apb...@ch... > [mailto:apb...@ch...]En nombre > de Nathan > A. Baker Enviado el: Miércoles, 20 de Agosto de 2003 08:07 a.m. > Para: Frank D Ducheneaux > CC: APBS Users > > > Hi Frank -- > > >1) I have been doing calculations on a group of small organic > >molecules (less than 40 atoms). I have been advised to use either a > >1.4 A or 0.0 A solvent radius (srad). Does anyone know which to use? > > This is anyone's guess -- I'd choose the surface definition > that gives you the best agreement with experiment. Recent > work by HX Zhou would suggest this should be the van der > Waals (srad 0.0) surface. > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > |