RE: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
Hi, I just ran grompp and it does not complain about anything (and no posre.itp file). Are you really sure there is no reference to posre.itp in your files? Try: grep posre *.itp *.top Berk > Subject: RE: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Wed, 5 Nov 2008 15:53:16 + > > On Wed, 2008-11-05 at 16:28 +0100, Berk Hess wrote: > > Hi, > > > > I just ran the 4.0 version of pdb2gmx on a multi-chain pdb file > > and posre.itp does not appear anywhere. > > When I've run pdb2gmx on my multi-chain pdb file I get posre_*.itp files > automatically because in my pdb file I have chain identifiers; I have > chain A and chain B, and Gromacs assumed chain C. That files was not > "hand made". > > Now I've tried to run pdb2gmx on the same pdb file, but without chain > identifiers and I get just one posre.itp file with all the information. > > But the real question is not that. Why is grompp asking for a posre.itp > file that's not declared anywhere? In the .top file I declared my > posre_*.itp files, so why is grompp ask me for posre.itp? And the > strange thing is that with a empty file everything is working now. > > Have you tried to run energy minimization on multi-chain system, having > no posre.itp file? > > Nuno Azoia > > > > > From the file names it seems that the files are non-standard > > and made of modified by hand. > > So maybe you somehow modified a file with posre.itp in it? > > > > Berk > > > > > > > Date: Wed, 5 Nov 2008 10:11:03 -0500 > > > From: [EMAIL PROTECTED] > > > To: [EMAIL PROTECTED]; gmx-users@gromacs.org > > > Subject: Re: [gmx-users] Problems with grompp and posre.itp in > > gromacs 4.0 > > > CC: > > > > > > > > > > > > Nuno Azoia wrote: > > > > On Wed, 2008-11-05 at 07:57 -0500, Justin A. Lemkul wrote: > > > >> Please remember to keep all correspondence on the list for > > archiving purposes. > > > >> Also, others out there may have information to contribute. > > > > > > > > Sorry about that. I just press Reply and I didn't check the e-mail > > > > address. > > > > > > > > I've solved the problem with your help. > > > > > > > > I've tried what you have told me but I get the same error message. > > > > Calling an .itp file within a .itp file always works with me (in > > version > > > > 3.3.1), but it makes more sense the way you describe, declaring > > > > everything in the .top file. > > > > > > > > The problem seems to be the posre.itp file itself. Even with the 3 > > files > > > > I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp > > needs a > > > > posre.itp file. So the solution was to create a empty posre.itp > > file. > > > > Now it's clear to me that my first option (see below the > > description of > > > > the first posre.itp file I've created) makes no sense because by > > that > > > > way I was calling each posre_*.itp file twice: once in the .top > > file and > > > > the other in posre.itp file. Grommp was reading the posre.itp file > > > > first, without any reference to any molecule, and it just don't > > work. > > > > > > > > > > Well, I'm glad it worked, but having to create an empty posre.itp > > file sounds a > > > bit nonsensical to me. Maybe the developers can help us out - has > > something > > > within grompp changed that makes a posre.itp file explicitly > > necessary? > > > > > > -Justin > > > > > > > Thank you very much! > > > > > > > > Nuno Azoia > > > > > > > >> Nuno Azoia wrote: > > > >>> Hi Justin. Tank you for your answer! > > > >>> > > > >>> Ok! I agree with you, and I'm doing something wrong. I just can > > > >>> understand what. Can you please help me a little more. > > > >>> > > > >>> In my .top file I have this lines > > > >>> > > > >>> --- > > > >>> ; Include chain topologies > > > >>> #include "krt_spd_C.itp" > > > >>> #include "krt_spd_A.itp" > > > >>> #in
RE: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
On Wed, 2008-11-05 at 16:28 +0100, Berk Hess wrote: > Hi, > > I just ran the 4.0 version of pdb2gmx on a multi-chain pdb file > and posre.itp does not appear anywhere. When I've run pdb2gmx on my multi-chain pdb file I get posre_*.itp files automatically because in my pdb file I have chain identifiers; I have chain A and chain B, and Gromacs assumed chain C. That files was not "hand made". Now I've tried to run pdb2gmx on the same pdb file, but without chain identifiers and I get just one posre.itp file with all the information. But the real question is not that. Why is grompp asking for a posre.itp file that's not declared anywhere? In the .top file I declared my posre_*.itp files, so why is grompp ask me for posre.itp? And the strange thing is that with a empty file everything is working now. Have you tried to run energy minimization on multi-chain system, having no posre.itp file? Nuno Azoia > > From the file names it seems that the files are non-standard > and made of modified by hand. > So maybe you somehow modified a file with posre.itp in it? > > Berk > > > > Date: Wed, 5 Nov 2008 10:11:03 -0500 > > From: [EMAIL PROTECTED] > > To: [EMAIL PROTECTED]; gmx-users@gromacs.org > > Subject: Re: [gmx-users] Problems with grompp and posre.itp in > gromacs 4.0 > > CC: > > > > > > > > Nuno Azoia wrote: > > > On Wed, 2008-11-05 at 07:57 -0500, Justin A. Lemkul wrote: > > >> Please remember to keep all correspondence on the list for > archiving purposes. > > >> Also, others out there may have information to contribute. > > > > > > Sorry about that. I just press Reply and I didn't check the e-mail > > > address. > > > > > > I've solved the problem with your help. > > > > > > I've tried what you have told me but I get the same error message. > > > Calling an .itp file within a .itp file always works with me (in > version > > > 3.3.1), but it makes more sense the way you describe, declaring > > > everything in the .top file. > > > > > > The problem seems to be the posre.itp file itself. Even with the 3 > files > > > I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp > needs a > > > posre.itp file. So the solution was to create a empty posre.itp > file. > > > Now it's clear to me that my first option (see below the > description of > > > the first posre.itp file I've created) makes no sense because by > that > > > way I was calling each posre_*.itp file twice: once in the .top > file and > > > the other in posre.itp file. Grommp was reading the posre.itp file > > > first, without any reference to any molecule, and it just don't > work. > > > > > > > Well, I'm glad it worked, but having to create an empty posre.itp > file sounds a > > bit nonsensical to me. Maybe the developers can help us out - has > something > > within grompp changed that makes a posre.itp file explicitly > necessary? > > > > -Justin > > > > > Thank you very much! > > > > > > Nuno Azoia > > > > > >> Nuno Azoia wrote: > > >>> Hi Justin. Tank you for your answer! > > >>> > > >>> Ok! I agree with you, and I'm doing something wrong. I just can > > >>> understand what. Can you please help me a little more. > > >>> > > >>> In my .top file I have this lines > > >>> > > >>> --- > > >>> ; Include chain topologies > > >>> #include "krt_spd_C.itp" > > >>> #include "krt_spd_A.itp" > > >>> #include "krt_spd_B.itp > > >>> --- > > >>> > > >>> > > >> That should be fine. > > >> > > >>> > > >>> The krt_spd_C.itp is the topology of a peptide with 244 atoms. > > >>> krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418 > atoms, > > >>> respectively. In the last line of each .itp file I have > something like > > >>> this (the letter changes with the corresponding file name) > > >>> > > >>> --- > > >>> ; Include Position restraint file > > >>> #ifdef POSRES > > >>> #include "posre_A.itp" > > >>> #endif > > &g
RE: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
Hi, I just ran the 4.0 version of pdb2gmx on a multi-chain pdb file and posre.itp does not appear anywhere. >From the file names it seems that the files are non-standard and made of modified by hand. So maybe you somehow modified a file with posre.itp in it? Berk > Date: Wed, 5 Nov 2008 10:11:03 -0500 > From: [EMAIL PROTECTED] > To: [EMAIL PROTECTED]; gmx-users@gromacs.org > Subject: Re: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0 > CC: > > > > Nuno Azoia wrote: > > On Wed, 2008-11-05 at 07:57 -0500, Justin A. Lemkul wrote: > >> Please remember to keep all correspondence on the list for archiving > >> purposes. > >> Also, others out there may have information to contribute. > > > > Sorry about that. I just press Reply and I didn't check the e-mail > > address. > > > > I've solved the problem with your help. > > > > I've tried what you have told me but I get the same error message. > > Calling an .itp file within a .itp file always works with me (in version > > 3.3.1), but it makes more sense the way you describe, declaring > > everything in the .top file. > > > > The problem seems to be the posre.itp file itself. Even with the 3 files > > I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp needs a > > posre.itp file. So the solution was to create a empty posre.itp file. > > Now it's clear to me that my first option (see below the description of > > the first posre.itp file I've created) makes no sense because by that > > way I was calling each posre_*.itp file twice: once in the .top file and > > the other in posre.itp file. Grommp was reading the posre.itp file > > first, without any reference to any molecule, and it just don't work. > > > > Well, I'm glad it worked, but having to create an empty posre.itp file sounds > a > bit nonsensical to me. Maybe the developers can help us out - has something > within grompp changed that makes a posre.itp file explicitly necessary? > > -Justin > > > Thank you very much! > > > > Nuno Azoia > > > >> Nuno Azoia wrote: > >>> Hi Justin. Tank you for your answer! > >>> > >>> Ok! I agree with you, and I'm doing something wrong. I just can > >>> understand what. Can you please help me a little more. > >>> > >>> In my .top file I have this lines > >>> > >>> --- > >>> ; Include chain topologies > >>> #include "krt_spd_C.itp" > >>> #include "krt_spd_A.itp" > >>> #include "krt_spd_B.itp > >>> --- > >>> > >>> > >> That should be fine. > >> > >>> > >>> The krt_spd_C.itp is the topology of a peptide with 244 atoms. > >>> krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418 atoms, > >>> respectively. In the last line of each .itp file I have something like > >>> this (the letter changes with the corresponding file name) > >>> > >>> --- > >>> ; Include Position restraint file > >>> #ifdef POSRES > >>> #include "posre_A.itp" > >>> #endif > >>> --- > >>> > >>> > >> This might be the problem. You're calling an .itp file from within an > >> .itp > >> file. That may work, but I've never tried it. Each .itp file should > >> provide > >> the parameters for a single molecule, no more. What I would try is the > >> following: > >> > >> ; Include chain topologies > >> #include "krt_spd_C.itp" > >> > >> #ifdef POSRES_C > >> #include "posre_C.itp" > >> #endif > >> > >> #include "krt_spd_A.itp" > >> > >> #ifdef POSRES_A > >> #include "posre_A.itp" > >> #endif > >> > >> #include "krt_spd_B.itp" > >> > >> #ifdef POSRES_B > >> #include "posre_B.itp" > >> #endif > >> > >> That way, each chain topology is followed by its corresponding position > >> restraint file, under the appropriate [ molecule ] definition. > >> > >> -Justin > >> > >>> > >>> Each posre_*.itp
Re: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
Nuno Azoia wrote: On Wed, 2008-11-05 at 07:57 -0500, Justin A. Lemkul wrote: Please remember to keep all correspondence on the list for archiving purposes. Also, others out there may have information to contribute. Sorry about that. I just press Reply and I didn't check the e-mail address. I've solved the problem with your help. I've tried what you have told me but I get the same error message. Calling an .itp file within a .itp file always works with me (in version 3.3.1), but it makes more sense the way you describe, declaring everything in the .top file. The problem seems to be the posre.itp file itself. Even with the 3 files I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp needs a posre.itp file. So the solution was to create a empty posre.itp file. Now it's clear to me that my first option (see below the description of the first posre.itp file I've created) makes no sense because by that way I was calling each posre_*.itp file twice: once in the .top file and the other in posre.itp file. Grommp was reading the posre.itp file first, without any reference to any molecule, and it just don't work. Well, I'm glad it worked, but having to create an empty posre.itp file sounds a bit nonsensical to me. Maybe the developers can help us out - has something within grompp changed that makes a posre.itp file explicitly necessary? -Justin Thank you very much! Nuno Azoia Nuno Azoia wrote: Hi Justin. Tank you for your answer! Ok! I agree with you, and I'm doing something wrong. I just can understand what. Can you please help me a little more. In my .top file I have this lines --- ; Include chain topologies #include "krt_spd_C.itp" #include "krt_spd_A.itp" #include "krt_spd_B.itp --- That should be fine. The krt_spd_C.itp is the topology of a peptide with 244 atoms. krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418 atoms, respectively. In the last line of each .itp file I have something like this (the letter changes with the corresponding file name) --- ; Include Position restraint file #ifdef POSRES #include "posre_A.itp" #endif --- This might be the problem. You're calling an .itp file from within an .itp file. That may work, but I've never tried it. Each .itp file should provide the parameters for a single molecule, no more. What I would try is the following: ; Include chain topologies #include "krt_spd_C.itp" #ifdef POSRES_C #include "posre_C.itp" #endif #include "krt_spd_A.itp" #ifdef POSRES_A #include "posre_A.itp" #endif #include "krt_spd_B.itp" #ifdef POSRES_B #include "posre_B.itp" #endif That way, each chain topology is followed by its corresponding position restraint file, under the appropriate [ molecule ] definition. -Justin Each posre_*.itp file has positions restraints for all the atoms in the peptide. For instance, posre_A.itp is something like this: --- ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 (...) 430 1 1000 1000 1000 433 1 1000 1000 1000 434 1 1000 1000 1000 435 1 1000 1000 1000 Ok. In version 3.3.1 that's all I used to do. But now version 4.0 demands a posre.itp file, an so I've created this one, and at least by this way grompp are reading my files ; Include posre topology #include "posre_A.itp" #include "posre_B.itp" #include "posre_C.itp" That's why I can not understand what I'm doing wrong. Another thing that I'm finding surprising is that, with two different systems, in two different simulations, I get the same error in the 15th position. Thank you for your time. Nuno Azoia On Tue, 2008-11-04 at 13:14 -0500, Justin A. Lemkul wrote: Quoting Nuno Azoia <[EMAIL PROTECTED]>: Hi! I'm having problems with grompp in version 4.0. When I attempt to run grompp I get this message. I've tried with two different systems, but the message is exactly the same --- Program grompp, VERSION 4.0 Source code file: toppush.c, line: 1196 Fatal error: [ file posre_A.itp, line 16 ]: Atom index (15) in position_restraints out of bounds (1-14). This probably means that you have inserted topology section "position_restraints" in a part belonging to a diff
Re: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
On Wed, 2008-11-05 at 07:57 -0500, Justin A. Lemkul wrote: > Please remember to keep all correspondence on the list for archiving > purposes. > Also, others out there may have information to contribute. Sorry about that. I just press Reply and I didn't check the e-mail address. I've solved the problem with your help. I've tried what you have told me but I get the same error message. Calling an .itp file within a .itp file always works with me (in version 3.3.1), but it makes more sense the way you describe, declaring everything in the .top file. The problem seems to be the posre.itp file itself. Even with the 3 files I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp needs a posre.itp file. So the solution was to create a empty posre.itp file. Now it's clear to me that my first option (see below the description of the first posre.itp file I've created) makes no sense because by that way I was calling each posre_*.itp file twice: once in the .top file and the other in posre.itp file. Grommp was reading the posre.itp file first, without any reference to any molecule, and it just don't work. Thank you very much! Nuno Azoia > > Nuno Azoia wrote: > > Hi Justin. Tank you for your answer! > > > > Ok! I agree with you, and I'm doing something wrong. I just can > > understand what. Can you please help me a little more. > > > > In my .top file I have this lines > > > > --- > > ; Include chain topologies > > #include "krt_spd_C.itp" > > #include "krt_spd_A.itp" > > #include "krt_spd_B.itp > > --- > > > > > > That should be fine. > > > > > > > The krt_spd_C.itp is the topology of a peptide with 244 atoms. > > krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418 atoms, > > respectively. In the last line of each .itp file I have something like > > this (the letter changes with the corresponding file name) > > > > --- > > ; Include Position restraint file > > #ifdef POSRES > > #include "posre_A.itp" > > #endif > > --- > > > > > > This might be the problem. You're calling an .itp file from within an .itp > file. That may work, but I've never tried it. Each .itp file should provide > the parameters for a single molecule, no more. What I would try is the > following: > > ; Include chain topologies > #include "krt_spd_C.itp" > > #ifdef POSRES_C > #include "posre_C.itp" > #endif > > #include "krt_spd_A.itp" > > #ifdef POSRES_A > #include "posre_A.itp" > #endif > > #include "krt_spd_B.itp" > > #ifdef POSRES_B > #include "posre_B.itp" > #endif > > That way, each chain topology is followed by its corresponding position > restraint file, under the appropriate [ molecule ] definition. > > -Justin > > > > > > > Each posre_*.itp file has positions restraints for all the atoms in the > > peptide. For instance, posre_A.itp is something like this: > > > > --- > > ; In this topology include file, you will find position restraint > > ; entries for all the heavy atoms in your original pdb file. > > ; This means that all the protons which were added by pdb2gmx are > > ; not restrained. > > > > [ position_restraints ] > > ; atom type fx fy fz > > 1 1 1000 1000 1000 > > 5 1 1000 1000 1000 > > 6 1 1000 1000 1000 > > (...) > >430 1 1000 1000 1000 > >433 1 1000 1000 1000 > >434 1 1000 1000 1000 > >435 1 1000 1000 1000 > > > > > > > > > > > > Ok. In version 3.3.1 that's all I used to do. But now version 4.0 > > demands a posre.itp file, an so I've created this one, and at least by > > this way grompp are reading my files > > > > > > ; Include posre topology > > #include "posre_A.itp" > > #include "posre_B.itp" > > #include "posre_C.itp" > > > > > > > > > > > > That's why I can not understand what I'm doing wrong. > > > > Another thing that I'm finding surprising is that, with two different > > systems, in two different simulations, I get the same error in the 15th > > position. > > > > Thank you for your time. > > > > Nuno Azoia > > > > > > > > On Tue, 2008-11-04 at 13:14 -0500, Justin A. Lemkul wrote: > >> Quoting Nuno Azoia <[EMAIL PROTECTED]>: > >> > >>> Hi! > >>> > >>> I'm having problems with grompp in version 4.0. > >>> When I attempt to run grompp I get this message. I've tried with two > >>> different systems, but the message is exactly the same > >>> > >>> --- > >>> Program grompp, VERSION 4.0 > >>> Source code file: toppush.c, line: 1196 > >>> > >>> Fatal
Re: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
Please remember to keep all correspondence on the list for archiving purposes. Also, others out there may have information to contribute. Nuno Azoia wrote: Hi Justin. Tank you for your answer! Ok! I agree with you, and I'm doing something wrong. I just can understand what. Can you please help me a little more. In my .top file I have this lines --- ; Include chain topologies #include "krt_spd_C.itp" #include "krt_spd_A.itp" #include "krt_spd_B.itp --- That should be fine. The krt_spd_C.itp is the topology of a peptide with 244 atoms. krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418 atoms, respectively. In the last line of each .itp file I have something like this (the letter changes with the corresponding file name) --- ; Include Position restraint file #ifdef POSRES #include "posre_A.itp" #endif --- This might be the problem. You're calling an .itp file from within an .itp file. That may work, but I've never tried it. Each .itp file should provide the parameters for a single molecule, no more. What I would try is the following: ; Include chain topologies #include "krt_spd_C.itp" #ifdef POSRES_C #include "posre_C.itp" #endif #include "krt_spd_A.itp" #ifdef POSRES_A #include "posre_A.itp" #endif #include "krt_spd_B.itp" #ifdef POSRES_B #include "posre_B.itp" #endif That way, each chain topology is followed by its corresponding position restraint file, under the appropriate [ molecule ] definition. -Justin Each posre_*.itp file has positions restraints for all the atoms in the peptide. For instance, posre_A.itp is something like this: --- ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 (...) 430 1 1000 1000 1000 433 1 1000 1000 1000 434 1 1000 1000 1000 435 1 1000 1000 1000 Ok. In version 3.3.1 that's all I used to do. But now version 4.0 demands a posre.itp file, an so I've created this one, and at least by this way grompp are reading my files ; Include posre topology #include "posre_A.itp" #include "posre_B.itp" #include "posre_C.itp" That's why I can not understand what I'm doing wrong. Another thing that I'm finding surprising is that, with two different systems, in two different simulations, I get the same error in the 15th position. Thank you for your time. Nuno Azoia On Tue, 2008-11-04 at 13:14 -0500, Justin A. Lemkul wrote: Quoting Nuno Azoia <[EMAIL PROTECTED]>: Hi! I'm having problems with grompp in version 4.0. When I attempt to run grompp I get this message. I've tried with two different systems, but the message is exactly the same --- Program grompp, VERSION 4.0 Source code file: toppush.c, line: 1196 Fatal error: [ file posre_A.itp, line 16 ]: Atom index (15) in position_restraints out of bounds (1-14). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. --- I'm not understanding why is "Atom index (15)" out of bounds. The range (1-14), where did it came from? grompp is finding a 15th atom to which it is trying to apply position restraints, but it is unable to. It seems that I just can only have 14 position_restaints conditions, but this don't make any sense to me. Can anyone help with this? What do I have to do to solve this problem? The error message is pretty clear - you have inserted #include "posre.itp" within the incorrect molecule definition (i.e., it is in the wrong order or wrong section in the .top). -Justin Tank you Nuno Azoia -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Textil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: [EMAIL PROTECTED] ___ 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 befo
Re: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0
Quoting Nuno Azoia <[EMAIL PROTECTED]>: > Hi! > > I'm having problems with grompp in version 4.0. > When I attempt to run grompp I get this message. I've tried with two > different systems, but the message is exactly the same > > --- > Program grompp, VERSION 4.0 > Source code file: toppush.c, line: 1196 > > Fatal error: > [ file posre_A.itp, line 16 ]: > Atom index (15) in position_restraints out of bounds (1-14). > This probably means that you have inserted topology section > "position_restraints" > in a part belonging to a different molecule than you intended to. > In that case move the "position_restraints" section to the right > molecule. > --- > > > I'm not understanding why is "Atom index (15)" out of bounds. The range > (1-14), where did it came from? grompp is finding a 15th atom to which it is trying to apply position restraints, but it is unable to. > It seems that I just can only have 14 position_restaints conditions, but > this don't make any sense to me. Can anyone help with this? What do I > have to do to solve this problem? > The error message is pretty clear - you have inserted #include "posre.itp" within the incorrect molecule definition (i.e., it is in the wrong order or wrong section in the .top). -Justin > Tank you > > Nuno Azoia > > -- > > Nuno Gonçalo Azoia Lopes > > Laboratório de Investigação em Acabamento > Departamento de Engenharia Textil > Universidade do Minho > Campus de Azurém > 4800-058 Guimarães > Portugal > > Tel: +351 253 510 280 - Ext: 517 289 > Fax: +351 253 510 293 > > Mobile: +351 965 382 487 > E-mail: [EMAIL PROTECTED] > > ___ > 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
Re: [gmx-users] Problems with GROMPP
> > >> I'd echo Justin's request for your *actual* commands. Computers are very > >> literal, and we'd rather have your original commands than something > >> that's clearly been filtered through your head. If the above reflects > >> your actual use of wildcards on the command line, that sounds like a > >> possible source of problems. > >> > >> Mark > > > > Of cause I didn't use those wildcards, but instead of the * I used > > the name of the file xxx, so that for pdb2gmx it reads > > ~$: ../bin/pdb2gmx -f ./xxx.pdb -o ./out -p ./out -q ./out.pdb -n > > ./out -i ./out > > > > In the meantime I've redone it several times and finally got some > > input files for grompp and mdrun (next problems ahead, but I try to > > solve them ;-) ) > > > > Jens > > Hi Jens, > When some people have already donated their time to assist you and > then you figure it out on your own, I suggest that you consider > posting a description of the actual problem and the solution that you > found. It will enhance your chances of getting a timely reply to your > next problem. > > Chris. Hi Chris, I'm really greatful for the help, and as I wrote I've just redone the things I did before... same input-files, same options. I don't know why it worked the last time I did it. All I know is that I had the problem with genbox which truncated the protein at different sites (in the xxx.gro file) and which then resulted in the problems with grompp because the xxx.top wasn't affected. Jens _ Unbegrenzter Speicherplatz für Ihr E-Mail Postfach? Jetzt aktivieren! http://www.digitaledienste.web.de/freemail/club/lp/?lp=7 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with GROMPP
> I'd echo Justin's request for your *actual* commands. Computers are very > literal, and we'd rather have your original commands than something > that's clearly been filtered through your head. If the above reflects > your actual use of wildcards on the command line, that sounds like a > possible source of problems. > > Mark Of cause I didn't use those wildcards, but instead of the * I used the name of the file xxx, so that for pdb2gmx it reads ~$: ../bin/pdb2gmx -f ./xxx.pdb -o ./out -p ./out -q ./out.pdb -n ./out -i ./out In the meantime I've redone it several times and finally got some input files for grompp and mdrun (next problems ahead, but I try to solve them ;-) ) Jens ___ GRATIS: Movie-FLAT. Jetzt freischalten! http://freemail.web.de/club/maxdome.htm ___ 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] Problems with GROMPP
Jens Pohl wrote: It might be helpful to post to the list the exact commands you issued so far. It might be illustrative of the problem. -Justin Tried it with bash and tcsh. pdb2gmx: -f *.pdb -o *.gro -p -q *.pdb -n -i opls-forcefield (no.6) editconf: -f *.gro -o -bt cubic -d 0.1 -vol genbox: -cp *.gro -cs (spc216-Water) -o -p results in truncated protein (different sites of truncation) I also tried different FFs with the same results. My protein is similar to 1MPY with only one chain to be simulated. I'd echo Justin's request for your *actual* commands. Computers are very literal, and we'd rather have your original commands than something that's clearly been filtered through your head. If the above reflects your actual use of wildcards on the command line, that sounds like a possible source of problems. Mark ___ 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] Problems with GROMPP
> It might be helpful to post to the list the exact commands you issued so far. > It might be illustrative of the problem. > > -Justin > Tried it with bash and tcsh. pdb2gmx: -f *.pdb -o *.gro -p -q *.pdb -n -i opls-forcefield (no.6) editconf: -f *.gro -o -bt cubic -d 0.1 -vol genbox: -cp *.gro -cs (spc216-Water) -o -p results in truncated protein (different sites of truncation) I also tried different FFs with the same results. My protein is similar to 1MPY with only one chain to be simulated. Jens _ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=0066 ___ 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] Problems with GROMPP
Quoting Jens Pohl <[EMAIL PROTECTED]>: > > > -Ursprüngliche Nachricht- > > Von: Discussion list for GROMACS users > > Gesendet: 12.01.08 03:29:49 > > An: Discussion list for GROMACS users > > Betreff: Re: [gmx-users] Problems with GROMPP > > > > > > > > > It seems, that my protein is truncated in the xxx.gro file. The number of > water molecules is ok, but there are about 150 AS residues missing after I > run GENBOX ??? The xxx.top has them included, so this explains the different > numbers. > > > > Well, read the warning messages from pdb2gmx, genbox and grompp carefully. > > > > Mark > > I didn't receive any warnings going through the single steps. No problem with > pdb2gmx. When I compare the *.gro to the original file there seems to be > everything ok. Same with editconf. (I rerun pdb3gmx and used -q to get a > *.pdb to compare to my original one). When I run genbox I get the *.top with > all residues, but the *.gro is truncated. Did it several times with the same > result...but no massage, that anything might be wrong (or I was too tired to > see it. Will do it again tomorrow) It might be helpful to post to the list the exact commands you issued so far. It might be illustrative of the problem. -Justin > > Jens > > > __ > Erweitern Sie FreeMail zu einem noch leistungsstärkeren E-Mail-Postfach! > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > ___ > 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
Re: [gmx-users] Problems with GROMPP
Jens Pohl wrote: -Ursprüngliche Nachricht- Von: Discussion list for GROMACS users Gesendet: 12.01.08 03:29:49 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] Problems with GROMPP It seems, that my protein is truncated in the xxx.gro file. The number of water molecules is ok, but there are about 150 AS residues missing after I run GENBOX ??? The xxx.top has them included, so this explains the different numbers. Well, read the warning messages from pdb2gmx, genbox and grompp carefully. Mark I didn't receive any warnings going through the single steps. No problem with pdb2gmx. When I compare the *.gro to the original file there seems to be everything ok. Same with editconf. (I rerun pdb3gmx and used -q to get a *.pdb to compare to my original one). When I run genbox I get the *.top with all residues, but the *.gro is truncated. Did it several times with the same result...but no massage, that anything might be wrong (or I was too tired to see it. Will do it again tomorrow) I'm not sure what the -q output does, but you can select the output format simply with the file extension, so pdb2gmx -c out.pdb. I can't think of a reason why genbox might truncate a molecule in a structure file. Mark ___ 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] Problems with GROMPP
> -Ursprüngliche Nachricht- > Von: Discussion list for GROMACS users > Gesendet: 12.01.08 03:29:49 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] Problems with GROMPP > > > > It seems, that my protein is truncated in the xxx.gro file. The number of > > water molecules is ok, but there are about 150 AS residues missing after I > > run GENBOX ??? The xxx.top has them included, so this explains the > > different numbers. > > Well, read the warning messages from pdb2gmx, genbox and grompp carefully. > > Mark I didn't receive any warnings going through the single steps. No problem with pdb2gmx. When I compare the *.gro to the original file there seems to be everything ok. Same with editconf. (I rerun pdb3gmx and used -q to get a *.pdb to compare to my original one). When I run genbox I get the *.top with all residues, but the *.gro is truncated. Did it several times with the same result...but no massage, that anything might be wrong (or I was too tired to see it. Will do it again tomorrow) Jens __ Erweitern Sie FreeMail zu einem noch leistungsstärkeren E-Mail-Postfach! Mehr Infos unter http://produkte.web.de/club/?mc=021131 ___ 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] Problems with GROMPP
It seems, that my protein is truncated in the xxx.gro file. The number of water molecules is ok, but there are about 150 AS residues missing after I run GENBOX ??? The xxx.top has them included, so this explains the different numbers. Well, read the warning messages from pdb2gmx, genbox and grompp carefully. Mark ___ 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] Problems with GROMPP
> -Ursprüngliche Nachricht- > Von: Discussion list for GROMACS users > Gesendet: 11.01.08 13:41:35 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] Problems with GROMPP > Jens Pohl wrote: > > Hello! > > > > I've tried to run GROMPP with a protein, following the flow-chart. > > Everything is working fine until I try to run the GROMPP program with the > > *.gro and *.top files I got from GENBOX (spc-water, cubic box, mdp like in > > the manual). The error is different numbers of coordinates in the two > > files. What to do??? I re-run the whole cascade several times, everytime > > ending up with this error. > > > Some atoms in your gro are probably not listed in the topology. So check > the number of water molecules, ions, etc and comare with your topology. > > To count the number of water molecules, use, e.g. > > grep SOL xxx.gro | grep -c OW > > Good luck, jochen > > > Thanks for you help > > Jens Thank you for your help! It seems, that my protein is truncated in the xxx.gro file. The number of water molecules is ok, but there are about 150 AS residues missing after I run GENBOX ??? The xxx.top has them included, so this explains the different numbers. Jens _ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=0066 ___ 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] Problems with GROMPP
Jens Pohl wrote: Hello! I've tried to run GROMPP with a protein, following the flow-chart. Everything is working fine until I try to run the GROMPP program with the *.gro and *.top files I got from GENBOX (spc-water, cubic box, mdp like in the manual). The error is different numbers of coordinates in the two files. What to do??? I re-run the whole cascade several times, everytime ending up with this error. Some atoms in your gro are probably not listed in the topology. So check the number of water molecules, ions, etc and comare with your topology. To count the number of water molecules, use, e.g. grep SOL xxx.gro | grep -c OW Good luck, jochen Thanks for you help Jens ___ Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=00 ___ 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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] Problems with GROMPP
Jens Pohl wrote: Hello! I've tried to run GROMPP with a protein, following the flow-chart. Everything is working fine until I try to run the GROMPP program with the *.gro and *.top files I got from GENBOX (spc-water, cubic box, mdp like in the manual). The error is different numbers of coordinates in the two files. What to do??? I re-run the whole cascade several times, everytime ending up with this error. So what are the numbers involved, and of what are they indicative? Mark ___ 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] Problems with GROMPP
Jens Pohl wrote: Hello! I've tried to run GROMPP with a protein, following the flow-chart. Everything is working fine until I try to run the GROMPP program with the *.gro and *.top files I got from GENBOX (spc-water, cubic box, mdp like in the manual). The error is different numbers of coordinates in the two files. What to do??? I re-run the whole cascade several times, everytime ending up with this error. error in your topology file. chapter 5 in the manual. Thanks for you help Jens ___ Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=00 ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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
