Re: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Justin, thank you very much for your attention. This is totally my fault. After putting N to the first residue, the column that indicates the coordinates has been flipped to the right. So, the first numbers could not be read by pdb2gmx. That is the source of the problem. However, thank you again. -Original Message- From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Mon, 31 Mar 2008 17:41:50 -0400 Subject: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Ok, it should be better to describe the problem in a more detailed way. > I got this structure from Swiss-modeler program. I do not think I have a > problem with the starting structure because I truncated the protein at some > PRO residue, and got no error at all. So, there is something wrong about the > nomenclature of the N terminus. I read things in the link, searched the web > and made some discussion with my friend, but I could not find the source of > the error :) So have I got it correct that you truncated the N-terminus originally, and are now adding residues back? It still suggests to me that you've generated a poor starting structure; the nomenclature should not be causing the issue. Identify which bonds pdb2gmx is warning you about (and the atoms involved), and evaluate them with a viewer (VMD, etc). Likely the model you've constructed has some non-physical attributes. -Justin > > Thank you Justin > > -Original Message- > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Date: Mon, 31 Mar 2008 15:25:11 -0400 > Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in > GROMACS > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > I already indicated the problem that I have. If I put an N prefix to the > > first residue, I get warning of having "long bonds." It has been indicated > in > > the mail.Moreover, these long bonds can not be minimized during the > > minimization step. Although I put a relatively higher tolerance for the > force > > on atoms. > > Alright, that makes more sense. You didn't say before that you couldn't > resolve > the long bonds by minimization. It seemed that you were asking again about > the > N-terminal nomenclature. It sounds like your starting structure has > problems, > but without knowing more I can't comment on that. Is it something you've > built, something from the RCSB, etc? > > Have a look at your structure and the mdrun output (md.log, in particular) to > see if you can determine where things are falling apart based on specific > warnings (LINCS, etc.) > > -Justin > > > > > -----Original Message- > > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > > To: Discussion list for GROMACS users > > Date: Mon, 31 Mar 2008 14:42:55 -0400 > > Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS > > > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > > > Hi all, > > > > > > I am trying to use AMBER ff in GROMACS. I have followed the steps that > are > > > given in the http://chemistry.csulb.edu/ffamber/ link. > > > > > > The first residue of the protein is GLN. I put an N prefix to this > residue. > > > The pdg2gmx works well except giving an warning of long bond between some > > > atoms. > > > > > > In contrast, if I have not put any prefix to GLN, then, the following > error > > > appears: > > > +++ > > > WARNING: atom H is missing in residue GLN 1 in the pdb file > > > You might need to add atom H to the hydrogen database of residue GLN > > > in the file ff???.hdb (see the manual) > > > > > > --- > > > Program pdb2gmx, VERSION 3.3.1 > > > Source code file: pdb2top.c, line: 697 > > > > > > Fatal error: > > > There were 1 missing atoms in molecule Protein, if you want to use this > > > incomplete topology anyhow, use the option -missing > > > +++ > > > > > > I looked at both the .rtp and .hdb files, but everything seems to be > > correct. > > > > > > Does anybody face with a similar problem? > > > > If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., > > NGLN), > > and likewise for C-terminal residues, CXXX. This is in the documentati
Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Ok, it should be better to describe the problem in a more detailed way. > I got this structure from Swiss-modeler program. I do not think I have a > problem with the starting structure because I truncated the protein at some > PRO residue, and got no error at all. So, there is something wrong about the > nomenclature of the N terminus. I read things in the link, searched the web > and made some discussion with my friend, but I could not find the source of > the error :) So have I got it correct that you truncated the N-terminus originally, and are now adding residues back? It still suggests to me that you've generated a poor starting structure; the nomenclature should not be causing the issue. Identify which bonds pdb2gmx is warning you about (and the atoms involved), and evaluate them with a viewer (VMD, etc). Likely the model you've constructed has some non-physical attributes. -Justin > > Thank you Justin > > -Original Message- > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Date: Mon, 31 Mar 2008 15:25:11 -0400 > Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in > GROMACS > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > I already indicated the problem that I have. If I put an N prefix to the > > first residue, I get warning of having "long bonds." It has been indicated > in > > the mail.Moreover, these long bonds can not be minimized during the > > minimization step. Although I put a relatively higher tolerance for the > force > > on atoms. > > Alright, that makes more sense. You didn't say before that you couldn't > resolve > the long bonds by minimization. It seemed that you were asking again about > the > N-terminal nomenclature. It sounds like your starting structure has > problems, > but without knowing more I can't comment on that. Is it something you've > built, something from the RCSB, etc? > > Have a look at your structure and the mdrun output (md.log, in particular) to > see if you can determine where things are falling apart based on specific > warnings (LINCS, etc.) > > -Justin > > > > > -Original Message- > > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > > To: Discussion list for GROMACS users > > Date: Mon, 31 Mar 2008 14:42:55 -0400 > > Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS > > > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > > > Hi all, > > > > > > I am trying to use AMBER ff in GROMACS. I have followed the steps that > are > > > given in the http://chemistry.csulb.edu/ffamber/ link. > > > > > > The first residue of the protein is GLN. I put an N prefix to this > residue. > > > The pdg2gmx works well except giving an warning of long bond between some > > > atoms. > > > > > > In contrast, if I have not put any prefix to GLN, then, the following > error > > > appears: > > > +++ > > > WARNING: atom H is missing in residue GLN 1 in the pdb file > > > You might need to add atom H to the hydrogen database of residue GLN > > > in the file ff???.hdb (see the manual) > > > > > > --- > > > Program pdb2gmx, VERSION 3.3.1 > > > Source code file: pdb2top.c, line: 697 > > > > > > Fatal error: > > > There were 1 missing atoms in molecule Protein, if you want to use this > > > incomplete topology anyhow, use the option -missing > > > +++ > > > > > > I looked at both the .rtp and .hdb files, but everything seems to be > > correct. > > > > > > Does anybody face with a similar problem? > > > > If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., > > NGLN), > > and likewise for C-terminal residues, CXXX. This is in the documentation > > from > > the AMBER ports at the link you cite above, and the link I already provided > > you. > > > > So what's the problem? > > > > -Justin > > > > > > > > Thanks in advance > > > Ozge Engin > > > = > > > Computational Science & Engineering > > > Koc University > > > ___ > > > gmx-users mailing listgmx-users@gromacs.org > > > ht
Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Ok, it should be better to describe the problem in a more detailed way. I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about the nomenclature of the N terminus. I read things in the link, searched the web and made some discussion with my friend, but I could not find the source of the error :) Thank you Justin -Original Message- From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Mon, 31 Mar 2008 15:25:11 -0400 Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > I already indicated the problem that I have. If I put an N prefix to the > first residue, I get warning of having "long bonds." It has been indicated in > the mail.Moreover, these long bonds can not be minimized during the > minimization step. Although I put a relatively higher tolerance for the force > on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin > > -Original Message- > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Date: Mon, 31 Mar 2008 14:42:55 -0400 > Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > Hi all, > > > > I am trying to use AMBER ff in GROMACS. I have followed the steps that are > > given in the http://chemistry.csulb.edu/ffamber/ link. > > > > The first residue of the protein is GLN. I put an N prefix to this residue. > > The pdg2gmx works well except giving an warning of long bond between some > > atoms. > > > > In contrast, if I have not put any prefix to GLN, then, the following error > > appears: > > +++ > > WARNING: atom H is missing in residue GLN 1 in the pdb file > > You might need to add atom H to the hydrogen database of residue GLN > > in the file ff???.hdb (see the manual) > > > > --- > > Program pdb2gmx, VERSION 3.3.1 > > Source code file: pdb2top.c, line: 697 > > > > Fatal error: > > There were 1 missing atoms in molecule Protein, if you want to use this > > incomplete topology anyhow, use the option -missing > > +++ > > > > I looked at both the .rtp and .hdb files, but everything seems to be > correct. > > > > Does anybody face with a similar problem? > > If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., > NGLN), > and likewise for C-terminal residues, CXXX. This is in the documentation > from > the AMBER ports at the link you cite above, and the link I already provided > you. > > So what's the problem? > > -Justin > > > > > Thanks in advance > > Ozge Engin > > = > > Computational Science & Engineering > > Koc University > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe reques
Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > I already indicated the problem that I have. If I put an N prefix to the > first residue, I get warning of having "long bonds." It has been indicated in > the mail.Moreover, these long bonds can not be minimized during the > minimization step. Although I put a relatively higher tolerance for the force > on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin > > -Original Message- > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Date: Mon, 31 Mar 2008 14:42:55 -0400 > Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > Hi all, > > > > I am trying to use AMBER ff in GROMACS. I have followed the steps that are > > given in the http://chemistry.csulb.edu/ffamber/ link. > > > > The first residue of the protein is GLN. I put an N prefix to this residue. > > The pdg2gmx works well except giving an warning of long bond between some > > atoms. > > > > In contrast, if I have not put any prefix to GLN, then, the following error > > appears: > > +++ > > WARNING: atom H is missing in residue GLN 1 in the pdb file > > You might need to add atom H to the hydrogen database of residue GLN > > in the file ff???.hdb (see the manual) > > > > --- > > Program pdb2gmx, VERSION 3.3.1 > > Source code file: pdb2top.c, line: 697 > > > > Fatal error: > > There were 1 missing atoms in molecule Protein, if you want to use this > > incomplete topology anyhow, use the option -missing > > +++ > > > > I looked at both the .rtp and .hdb files, but everything seems to be > correct. > > > > Does anybody face with a similar problem? > > If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., > NGLN), > and likewise for C-terminal residues, CXXX. This is in the documentation > from > the AMBER ports at the link you cite above, and the link I already provided > you. > > So what's the problem? > > -Justin > > > > > Thanks in advance > > Ozge Engin > > = > > Computational Science & Engineering > > Koc University > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > Ozge Engin > = > Computational Science & Engineering > Koc University > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ===
Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having "long bonds." It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. -Original Message- From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Hi all, > > I am trying to use AMBER ff in GROMACS. I have followed the steps that are > given in the http://chemistry.csulb.edu/ffamber/ link. > > The first residue of the protein is GLN. I put an N prefix to this residue. > The pdg2gmx works well except giving an warning of long bond between some > atoms. > > In contrast, if I have not put any prefix to GLN, then, the following error > appears: > +++ > WARNING: atom H is missing in residue GLN 1 in the pdb file > You might need to add atom H to the hydrogen database of residue GLN > in the file ff???.hdb (see the manual) > > --- > Program pdb2gmx, VERSION 3.3.1 > Source code file: pdb2top.c, line: 697 > > Fatal error: > There were 1 missing atoms in molecule Protein, if you want to use this > incomplete topology anyhow, use the option -missing > +++ > > I looked at both the .rtp and .hdb files, but everything seems to be correct. > > Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin > > Thanks in advance > Ozge Engin > = > Computational Science & Engineering > Koc University > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Hi all, > > I am trying to use AMBER ff in GROMACS. I have followed the steps that are > given in the http://chemistry.csulb.edu/ffamber/ link. > > The first residue of the protein is GLN. I put an N prefix to this residue. > The pdg2gmx works well except giving an warning of long bond between some > atoms. > > In contrast, if I have not put any prefix to GLN, then, the following error > appears: > +++ > WARNING: atom H is missing in residue GLN 1 in the pdb file > You might need to add atom H to the hydrogen database of residue GLN > in the file ff???.hdb (see the manual) > > --- > Program pdb2gmx, VERSION 3.3.1 > Source code file: pdb2top.c, line: 697 > > Fatal error: > There were 1 missing atoms in molecule Protein, if you want to use this > incomplete topology anyhow, use the option -missing > +++ > > I looked at both the .rtp and .hdb files, but everything seems to be correct. > > Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin > > Thanks in advance > Ozge Engin > = > Computational Science & Engineering > Koc University > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
