Re: [gmx-users] error with changing pdb file
ksm tprk wrote: Hi Justin, I got same error before. The solution is still the same. You have listed all of your carbon atom types as simply "C" which corresponds to a bare carbon (carbonyl, etc) and if you search in ffgmxbon.itp for an angle involving three of these atoms, you won't find any. Choose a suitable atom type for these atoms and look for available parameters in ffgmxbon.itp. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: Hi Justin, I will try to be more clear. What I did, first I created a carbon nanotube using Tubegen carbon nanotube generator. After that I changed one carbon atom with another atom using text editor. My ffgmx file is same as what http://cs86.com/CNSE/SWNT.htm has. Next I created .top by applying ffgmx.n2t force field and .gro file respectively. And I used grompp to run my simulation. And What I got the error is: OK, the problem is pretty straightforward now. You have a nitrogen atom within a CNT, and there are no suitable angle parameters for such a system. The atom type chosen is simply "N," which (from the ffgmx.atp file) corresponds to a peptide nitrogen in an amide, which is not what is present in your system so this assignment is incorrect. Perhaps "NR6" might be more appropriate? -Justin creating statusfile for 8 nodes... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling cpp... processing topology... Generated 1282 of the 1485 non-bonded parameter combinations WARNING 1 [file "cnt80.top", line 11144]: No default Angle types, using zeroes WARNING 2 [file "cnt80.top", line 11144]: No default Angle types for perturbed atoms, using normal values WARNING 3 [file "cnt80.top", line 11145]: No default Angle types, using zeroes WARNING 4 [file "cnt80.top", line 11145]: No default Angle types for perturbed atoms, using normal values WARNING 5 [file "cnt80.top", line 11187]: No default Angle types, using zeroes WARNING 6 [file "cnt80.top", line 11187]: No default Angle types for perturbed atoms, using normal values WARNING 7 [file "cnt80.top", line 11189]: No default Angle types, using zeroes WARNING 8 [file "cnt80.top", line 11189]: No default Angle types for perturbed atoms, using normal values WARNING 9 [file "cnt80.top", line 11190]: No default Angle types, using zeroes WARNING 10 [file "cnt80.top", line 11190]: No default Angle types for perturbed atoms, using normal values Cleaning up temporary file grompp5QOA9q --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 The error atom is 25th atom. and the error lines specified in topology file are( I underlined and made bold them): . [ angles ] ; aiajak functc0c1c2 c3 2 120 1 1 2 3 1 2 3 4 1 2 322 1 4 322 1 3 4 5 1 * 3 425 1* *5 425 1* * * 4 5 6 1 5 6 7 1 6 7 8 1 6 726 1 8 726 1 7 8 9 1 7 829 1 9 829 1 8 910 1 91011 1 101112 1 101130 1 121130 1 111213 1 111233 1 131233 1 121314 1 131415 1 141516 1 141534 1 161534 1 151617 1 151637 1 171637 1 161718 1 171819 1 181920 1 181938 1 201938 1 12019 1 12021 1 192021 1 202122 1 202140 1 222140 1 32221 1 32223 1 212223 1 222324 1 222342 1 242342 1 * 232425 1* 232445 1 *252445 1* *42524 1* 42526 1 242526 1 72625 1 . I attached topology and coordinate files too. I am sorry that I gave not enough information. Thank you, Kasim > I can't keep trying to help you if you don't provide relevant information. If > you want free help, you have to make it easy for those trying to help you. This > topology snippet is not at all what I asked to see. To be clear, please post > the following information: > > 1. The lines from the topology specified in the grompp error messages (the line > numbers are given in the error messages) > 2. The coordinate file entries that correspond to the atoms on those lines. It > would be helpful to see the coordinate file that works, as well as the one that > was modified that no longer works. > > Going back to your very first post, the root of the problem is that there are > not bonded parameters in the ffgmx force field to describe whatever changes you > made. Since you have yet to actually demonstrate what these changes were and > how the affected the topology, there is no better help that anyone can provide. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILE
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: Hello Justin, I used ffgmx.n2t gromacs force field. and my topology file is: ; ; This is your include topology file ; Generated by x2top ; ; Include forcefield parameters #include "ffgmx.itp" [ moleculetype ] ; Namenrexcl ICE 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 C 1UNK C 0 0 12.011 C 0 0 ; qtot 0 2 C 1UNK C 1 0 12.011 C 0 0 ; qtot 0 3 C 1UNK C 2 . 24 C 1UNK C 23 0 12.011 C 0 0 ; qtot 0 25 N 1UNK N 24 014.0067 N 0 0 ; qtot 0 26 C 1UNK C 25 0 12.011 C 0 0 ; qtot 0 .. Thank you helping me, I can't keep trying to help you if you don't provide relevant information. If you want free help, you have to make it easy for those trying to help you. This topology snippet is not at all what I asked to see. To be clear, please post the following information: 1. The lines from the topology specified in the grompp error messages (the line numbers are given in the error messages) 2. The coordinate file entries that correspond to the atoms on those lines. It would be helpful to see the coordinate file that works, as well as the one that was modified that no longer works. Going back to your very first post, the root of the problem is that there are not bonded parameters in the ffgmx force field to describe whatever changes you made. Since you have yet to actually demonstrate what these changes were and how the affected the topology, there is no better help that anyone can provide. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: Hello Justin, I looked at in my gromacs/3.3.1 and it ahs only ffgmx.n2t force field file. because of that, I chaged to new version gromacs. I tried to use different force filed but new version gromacs but they didn't work. I used gromacs/4.0.5 and I created .gro and by using x2top but it give below errors. If I use pdb2gmx, it gives me residue UNK error. First I used "GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)" but it gave me below error: Can not find forcefield for atom C-1597 with 3 bonds Can not find forcefield for atom C-1598 with 3 bonds Can not find forcefield for atom C-1599 with 2 bonds Can not find forcefield for atom C-1600 with 2 bonds --- Program x2top_mpi, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a forcefield type for 0 out of 1600 atoms --- After that I used "OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)" and it gave me: Looking whether force field files exist Opening library file /opt/apps/gromacs/4.0.5/share/gromacs/top/ffoplsaa.rtp Opening library file ffoplsaa.n2t Opening library file ffoplsaa.n2t There are 25 name to type translations Generating bonds from distances... atom 1600 Can not find forcefield for atom N-25 with 3 bonds --- Program x2top_mpi, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a forcefield type for 1599 out of 1600 atoms --- And I tried "[DEPRECATED] Gromacs force field (see manual)" and "Encad all-atom force field, using scaled-down vacuum charges". they gave me same error at first. The 4.0.5 version of x2top is broken unless you use the -nopbc option, which, for the purposes of carbon nanotubes, is useless unless you specify all the cross-boundary bonded terms yourself. You had a functional topology before, why are you starting over? You didn't give a very clear description of the changes you were making that were inducing the grompp errors, and you stand a better chance of identifying those problems and solving them if you provide the information I asked for last time (relevant topology lines and the corresponding coordinate entries). -Justin Thank you, Kasim > Date: Thu, 17 Dec 2009 15:31:23 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error with changing pdb file > > > > ksm tprk wrote: > > I changed pdb file after that I generated topology file. > > > > It appears you are relying on grompp to figure out what parameters should be > used for these angles, and apparently, given these atom types, there are no > default values available in the force field you've chosen to use. So either > specify parameters manually or use a different force field. > > If you need further advice, it would be useful to know the force field you're > trying to use and see the problematic lines of the topology alongside the > modified coordinate file. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hotmail: Powerful Free email with security by Microsoft. Get it now. <http://clk.atdmt.com/GBL/go/171222986/direct/01/> -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: I changed pdb file after that I generated topology file. It appears you are relying on grompp to figure out what parameters should be used for these angles, and apparently, given these atom types, there are no default values available in the force field you've chosen to use. So either specify parameters manually or use a different force field. If you need further advice, it would be useful to know the force field you're trying to use and see the problematic lines of the topology alongside the modified coordinate file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: Hello, While I am simulating my simulations, I encountered below error. I have pdb file which is: HEADERPROTEIN TITLE (5,5) Nanotube (1,1,80) replication AUTHORTubeGen 3.3, J T Frey, University of Delaware EXPDTATHEORETICAL MODEL ATOM 1 C UNK 1 3.410 0.000 -98.494 1.00 0.00 ATOM 2 C UNK 1 3.113 1.390 -98.494 1.00 0.00 ATOM 3 C UNK 1 2.758 2.004 -97.263 1.00 0.00 ATOM 4 C UNK 1 1.702 2.954 -97.263 1.00 0.00 ATOM 5 C UNK 1 1.054 3.243 -98.494 1.00 0.00 ATOM 6 C UNK 1 -0.360 3.391 -98.494 1.00 0.00 ATOM 7 C UNK 1 -1.054 3.243 -97.263 1.00 0.00 ATOM 8 C UNK 1 -2.284 2.532 -97.263 1.00 0.00 ATOM 9 C UNK 1 -2.758 2.004 -98.494 1.00 0.00 ... CONECT 1596 1595 1597 CONECT 1597 1576 1596 1598 CONECT 1598 1579 1597 1599 CONECT 1599 1598 1600 CONECT 1600 1581 1599 MASTER00000000 16000 16000 END But by using text editor, I change an atom with another atom. And I created .top and .gro files respectively. ( my sample is basically similar to Christopher Stiles' work, http://cs86.com/CNSE/SWNT.htm) After I run my simulation, it gives the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling cpp... processing topology... Generated 1282 of the 1485 non-bonded parameter combinations WARNING 1 [file "cnt_500.top", line 72238]: No default Angle types, using zeroes WARNING 2 [file "cnt_500.top", line 72238]: No default Angle types for perturbed atoms, using normal values WARNING 3 [file "cnt_500.top", line 72239]: No default Angle types, using zeroes WARNING 4 [file "cnt_500.top", line 72239]: No default Angle types for perturbed atoms, using normal values WARNING 5 [file "cnt_500.top", line 72240]: No default Angle types, using zeroes WARNING 6 [file "cnt_500.top", line 72240]: No default Angle types for perturbed atoms, using normal values WARNING 7 [file "cnt_500.top", line 72241]: No default Angle types, using zeroes WARNING 8 [file "cnt_500.top", line 72241]: No default Angle types for perturbed atoms, using normal values WARNING 9 [file "cnt_500.top", line 72242]: No default Angle types, using zeroes WARNING 10 [file "cnt_500.top", line 72242]: No default Angle types for perturbed atoms, using normal values Cleaning up temporary file gromppYFxvHw --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp_mpi terminated --- Without changing my pdb file, there was no error but after I can an atom with another, I got above error. Is there anyone who had same problem before? I will really appreciate if you can help me. If you have altered the atom numbers or types without re-generating the topology, then the angles in the topology will no longer make sense. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error with changing pdb file
Hello, While I am simulating my simulations, I encountered below error. I have pdb file which is: HEADERPROTEINTITLE (5,5) Nanotube (1,1,80) replicationAUTHORTubeGen 3.3, J T Frey, University of DelawareEXPDTATHEORETICAL MODELATOM 1 C UNK 1 3.410 0.000 -98.494 1.00 0.00ATOM 2 C UNK 1 3.113 1.390 -98.494 1.00 0.00ATOM 3 C UNK 1 2.758 2.004 -97.263 1.00 0.00ATOM 4 C UNK 1 1.702 2.954 -97.263 1.00 0.00ATOM 5 C UNK 1 1.054 3.243 -98.494 1.00 0.00ATOM 6 C UNK 1 -0.360 3.391 -98.494 1.00 0.00ATOM 7 C UNK 1 -1.054 3.243 -97.263 1.00 0.00ATOM 8 C UNK 1 -2.284 2.532 -97.263 1.00 0.00ATOM 9 C UNK 1 -2.758 2.004 -98.494 1.00 0.00... CONECT 1596 1595 1597CONECT 1597 1576 1596 1598CONECT 1598 1579 1597 1599CONECT 1599 1598 1600CONECT 1600 1581 1599MASTER000000 00 16000 16000END But by using text editor, I change an atom with another atom.And I created .top and .gro files respectively.( my sample is basically similar to Christopher Stiles' work, http://cs86.com/CNSE/SWNT.htm) After I run my simulation, it gives the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#checking input for internal consistency...calling cpp...processing topology...Generated 1282 of the 1485 non-bonded parameter combinationsWARNING 1 [file "cnt_500.top", line 72238]: No default Angle types, using zeroesWARNING 2 [file "cnt_500.top", line 72238]: No default Angle types for perturbed atoms, using normal valuesWARNING 3 [file "cnt_500.top", line 72239]: No default Angle types, using zeroesWARNING 4 [file "cnt_500.top", line 72239]: No default Angle types for perturbed atoms, using normal valuesWARNING 5 [file "cnt_500.top", line 72240]: No default Angle types, using zeroesWARNING 6 [file "cnt_500.top", line 72240]: No default Angle types for perturbed atoms, using normal valuesWARNING 7 [file "cnt_500.top", line 72241]: No default Angle types, using zeroesWARNING 8 [file "cnt_500.top", line 72241]: No default Angle types for perturbed atoms, using normal valuesWARNING 9 [file "cnt_500.top", line 72242]: No default Angle types, using zeroesWARNING 10 [file "cnt_500.top", line 72242]: No default Angle types for perturbed atoms, using normal valuesCleaning up temporary file gromppYFxvHw---Program grompp_mpi, VERSION 3.3.1Source code file: fatal.c, line: 416 Fatal error:Too many warnings, grompp_mpi terminated--- Without changing my pdb file, there was no error but after I can an atom with another, I got above error.Is there anyone who had same problem before? I will really appreciate if you can help me. Thank you,Kasim _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
