Re: [gmx-users] missing of methyl at N-terminal
I have had trouble capping N- and C- terminal residues using the 3.3.X series of GROMACS. I even think I started a thread about it. Before you digg that thread up you should: i) work out what you want to do ii) understand what result you should get iii) do it and check it !!! If that fails I suggest you search the list for archives for threads discussing capping problems. For the record I got around the problem using pdb2gmx from the 3.2 or 3.1 series of GROMACS. Cheers Mitch Mark Abraham wrote: Bhawana Gupta wrote: hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. Terminology is important to get right. You were capping the *C-terminal* end with an *N-methyl*. * i m using forcefield ffgmx. That's a poor idea for anything other than a learning exercise. That force field has been deprecated for years. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as: - Program pdb2gmx, VERSION 4.0 Source code file: pdb2top.c, line: 574 Fatal error: atom N not found in residue 1ACE while combining tdb and rtp - This is my pdb file in text editor So what were your pdb2gmx command line and responses to prompts? You need to think carefully about why pdb2gmx might be looking for an N atom in your ACE residue that doesn't have one. 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 ___ 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] missing of methyl at N-terminal
Bhawana Gupta wrote: hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. Terminology is important to get right. You were capping the *C-terminal* end with an *N-methyl*. * i m using forcefield ffgmx. That's a poor idea for anything other than a learning exercise. That force field has been deprecated for years. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as: - Program pdb2gmx, VERSION 4.0 Source code file: pdb2top.c, line: 574 Fatal error: atom N not found in residue 1ACE while combining tdb and rtp - This is my pdb file in text editor So what were your pdb2gmx command line and responses to prompts? You need to think carefully about why pdb2gmx might be looking for an N atom in your ACE residue that doesn't have one. 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] missing of methyl at N-terminal
hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. * i m using forcefield ffgmx. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as: - Program pdb2gmx, VERSION 4.0 Source code file: pdb2top.c, line: 574 Fatal error: atom N not found in residue 1ACE while combining tdb and rtp - This is my pdb file in text editor AUTHORGENERATED BY OPEN BABEL 2.2.0 ATOM 1 CA ACE 1 -3.811 -0.502 0.471 1.00 0.00 C ATOM 2 C ACE 1 -2.354 -0.410 0.072 1.00 0.00 C ATOM 3 O ACE 1 -1.743 -1.403 -0.345 1.00 0.00 O ATOM 4 N ALA 2 -1.649 0.885 0.183 1.00 0.00 N ATOM 5 CA ALA 2 -0.244 1.035 -0.187 1.00 0.00 C ATOM 6 C ALA 2 0.221 2.456 0.023 1.00 0.00 C ATOM 7 O ALA 2 -0.530 3.334 0.466 1.00 0.00 O ATOM 8 CB ALA 2 -0.094 0.568 -1.645 1.00 0.00 C ATOM 9 N ALA 3 1.482 2.703 -0.281 1.00 0.00 N ATOM 10 CA ALA 3 2.069 4.031 -0.129 1.00 0.00 C ATOM 11 C ALA 3 3.519 4.033 -0.548 1.00 0.00 C ATOM 12 O ALA 3 4.081 3.015 -0.969 1.00 0.00 O ATOM 13 CB ALA 3 1.870 4.463 1.334 1.00 0.00 C ATOM 14 N ALA 4 4.149 5.189 -0.449 1.00 0.00 N ATOM 15 CA ALA 4 5.553 5.340 -0.819 1.00 0.00 C ATOM 16 C ALA 4 6.019 6.761 -0.609 1.00 0.00 C ATOM 17 O ALA 4 5.267 7.638 -0.166 1.00 0.00 O ATOM 18 CB ALA 4 5.704 4.872 -2.277 1.00 0.00 C ATOM 19 N ALA 5 7.279 7.008 -0.913 1.00 0.00 N ATOM 20 CA ALA 5 7.866 8.336 -0.760 1.00 0.00 C ATOM 21 C ALA 5 9.317 8.337 -1.179 1.00 0.00 C ATOM 22 O ALA 5 9.879 7.319 -1.601 1.00 0.00 O ATOM 23 CB ALA 5 7.668 8.768 0.703 1.00 0.00 C ATOM 24 N NAC 6 10.022 9.633 -1.069 1.00 0.00 N ATOM 25 CA NAC 6 11.417 9.736 -1.462 1.00 0.00 C CONECT12 CONECT2341 CONECT32 CONECT452 CONECT5864 CONECT6957 CONECT76 CONECT85 CONECT9 106 CONECT 10 119 13 CONECT 11 12 14 10 CONECT 12 11 CONECT 13 10 CONECT 14 15 11 CONECT 15 18 16 14 CONECT 16 19 15 17 CONECT 17 16 CONECT 18 15 CONECT 19 20 16 CONECT 20 21 19 23 CONECT 21 22 24 20 CONECT 22 21 CONECT 23 20 CONECT 24 25 21 CONECT 25 24 MASTER00000000 250 250 END so pls help me out. i had taken my pdb file from INSIGHTII program. With Regards Bhawana ___ 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] missing of methyl at N-terminal
Bhawana Gupta wrote: thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms while sorting atoms So from this you can work out that pdb2gmx is guessing that residue 6 (named "NHM" in your pdb file) is intended to be an NH2 residue (which has 3 atoms), but then gets confused trying to match one of them to the C atom in the residue named "NHM". You need to name residues according to the names in the .rtp database. Here, "NHM" presumably isn't right for N-methylamine your force field. Go and look up what it should be and edit your input to help pdb2gmx along. Computers can't be programmed to guess correctly in all cases what the user meant. You need to take some responsibility for telling it useful things :-) A good working knowledge of the contents of chapter 5 of the manual is invaluable here. 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] missing of methyl at N-terminal
Bhawana Gupta wrote: thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms while sorting atoms This probably comes about because you are trying to use parameters from an -NH2 group on a structure that contains -NH(CH3). You also haven't mentioned which force field you're trying to use. Some force fields do not have an N-methyl group parameterized (check the .rtp file). -Justin this is my pdb in text editor there is a presence of 25 atom in my pdb (C in residue NH2 6), but i m getting the error mentioned above AUTHORGENERATED BY OPEN BABEL 2.2.0 ATOM 1 CA ACE 1 -3.811 -0.502 0.471 1.00 0.00 C ATOM 2 C ACE 1 -2.354 -0.410 0.072 1.00 0.00 C ATOM 3 O ACE 1 -1.743 -1.403 -0.345 1.00 0.00 O ATOM 4 N ALA 2 -1.649 0.885 0.183 1.00 0.00 N ATOM 5 CA ALA 2 -0.244 1.035 -0.187 1.00 0.00 C ATOM 6 C ALA 2 0.221 2.456 0.023 1.00 0.00 C ATOM 7 O ALA 2 -0.530 3.334 0.466 1.00 0.00 O ATOM 8 CB ALA 2 -0.094 0.568 -1.645 1.00 0.00 C ATOM 9 N ALA 3 1.482 2.703 -0.281 1.00 0.00 N ATOM 10 CA ALA 3 2.069 4.031 -0.129 1.00 0.00 C ATOM 11 C ALA 3 3.519 4.033 -0.548 1.00 0.00 C ATOM 12 O ALA 3 4.081 3.015 -0.969 1.00 0.00 O ATOM 13 CB ALA 3 1.870 4.463 1.334 1.00 0.00 C ATOM 14 N ALA 4 4.149 5.189 -0.449 1.00 0.00 N ATOM 15 CA ALA 4 5.553 5.340 -0.819 1.00 0.00 C ATOM 16 C ALA 4 6.019 6.761 -0.609 1.00 0.00 C ATOM 17 O ALA 4 5.267 7.638 -0.166 1.00 0.00 O ATOM 18 CB ALA 4 5.704 4.872 -2.277 1.00 0.00 C ATOM 19 N ALA 5 7.279 7.008 -0.913 1.00 0.00 N ATOM 20 CA ALA 5 7.866 8.336 -0.760 1.00 0.00 C ATOM 21 C ALA 5 9.317 8.337 -1.179 1.00 0.00 C ATOM 22 O ALA 5 9.879 7.319 -1.601 1.00 0.00 O ATOM 23 CB ALA 5 7.668 8.768 0.703 1.00 0.00 C ATOM 24 N NHM 6 10.022 9.633 -1.069 1.00 0.00 N ATOM 25 C NHM 6 11.417 9.736 -1.462 1.00 0.00 C CONECT12 CONECT2341 CONECT32 CONECT452 CONECT5864 CONECT6957 CONECT76 CONECT85 CONECT9 106 CONECT 10 119 13 CONECT 11 12 14 10 CONECT 12 11 CONECT 13 10 CONECT 14 15 11 CONECT 15 18 16 14 CONECT 16 19 15 17 CONECT 17 16 CONECT 18 15 CONECT 19 20 16 CONECT 20 21 19 23 CONECT 21 22 24 20 CONECT 22 21 CONECT 23 20 CONECT 24 25 21 CONECT 25 24 MASTER00000000 250 250 END Please help me out. With regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive
Re: [gmx-users] missing of methyl at N-terminal
thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms while sorting atoms this is my pdb in text editor there is a presence of 25 atom in my pdb (C in residue NH2 6), but i m getting the error mentioned above AUTHORGENERATED BY OPEN BABEL 2.2.0 ATOM 1 CA ACE 1 -3.811 -0.502 0.471 1.00 0.00 C ATOM 2 C ACE 1 -2.354 -0.410 0.072 1.00 0.00 C ATOM 3 O ACE 1 -1.743 -1.403 -0.345 1.00 0.00 O ATOM 4 N ALA 2 -1.649 0.885 0.183 1.00 0.00 N ATOM 5 CA ALA 2 -0.244 1.035 -0.187 1.00 0.00 C ATOM 6 C ALA 2 0.221 2.456 0.023 1.00 0.00 C ATOM 7 O ALA 2 -0.530 3.334 0.466 1.00 0.00 O ATOM 8 CB ALA 2 -0.094 0.568 -1.645 1.00 0.00 C ATOM 9 N ALA 3 1.482 2.703 -0.281 1.00 0.00 N ATOM 10 CA ALA 3 2.069 4.031 -0.129 1.00 0.00 C ATOM 11 C ALA 3 3.519 4.033 -0.548 1.00 0.00 C ATOM 12 O ALA 3 4.081 3.015 -0.969 1.00 0.00 O ATOM 13 CB ALA 3 1.870 4.463 1.334 1.00 0.00 C ATOM 14 N ALA 4 4.149 5.189 -0.449 1.00 0.00 N ATOM 15 CA ALA 4 5.553 5.340 -0.819 1.00 0.00 C ATOM 16 C ALA 4 6.019 6.761 -0.609 1.00 0.00 C ATOM 17 O ALA 4 5.267 7.638 -0.166 1.00 0.00 O ATOM 18 CB ALA 4 5.704 4.872 -2.277 1.00 0.00 C ATOM 19 N ALA 5 7.279 7.008 -0.913 1.00 0.00 N ATOM 20 CA ALA 5 7.866 8.336 -0.760 1.00 0.00 C ATOM 21 C ALA 5 9.317 8.337 -1.179 1.00 0.00 C ATOM 22 O ALA 5 9.879 7.319 -1.601 1.00 0.00 O ATOM 23 CB ALA 5 7.668 8.768 0.703 1.00 0.00 C ATOM 24 N NHM 6 10.022 9.633 -1.069 1.00 0.00 N ATOM 25 C NHM 6 11.417 9.736 -1.462 1.00 0.00 C CONECT12 CONECT2341 CONECT32 CONECT452 CONECT5864 CONECT6957 CONECT76 CONECT85 CONECT9 106 CONECT 10 119 13 CONECT 11 12 14 10 CONECT 12 11 CONECT 13 10 CONECT 14 15 11 CONECT 15 18 16 14 CONECT 16 19 15 17 CONECT 17 16 CONECT 18 15 CONECT 19 20 16 CONECT 20 21 19 23 CONECT 21 22 24 20 CONECT 22 21 CONECT 23 20 CONECT 24 25 21 CONECT 25 24 MASTER00000000 250 250 END Please help me out. With regards Bhawana ___ 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] missing of methyl at N-terminal
Bhawana Gupta wrote: hello everyone, for doing peptide with usual amino acid simulation. i m bringing my *.pdb file from insightII as i dont know any other tool or software from where i can get any pdb file (model peptide-Eg. Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by using pdb2gmx. it give error that no C is present at 6 NH2 position. tell me what to do. Don't interpret error messages when reporting a problem with them to the list. If your interpretation was good, then you probably wouldn't have the problem. We'll be much more helpful if you give the actual input and (relevant) output copied and pasted from your terminal window. I shouldn't have to be guessing what actual problem means "it give error that no C is present at 6 NH2 position". In practice, InsightII uses PDB atom naming conventions that differ from GROMACS ones. For small cases your best solution is to use it to generate a PDB file, see what pdb2gmx doesn't like about it, refer to the forcefield .rtp files (see chapter 5 of the manual) and fix them with a text editor. If that becomes too tedious to be practical, invest in writing some sed or Perl scripts to automate the conversion. either tell me the name of free software or tool from where i can get the pdb of model peptide. Some options are given here http://wiki.gromacs.org/index.php/Coordinate_File but the world seems to be lacking a good, free solution. tell me one more thing that whether gromacs only take those pdb's which are converted by babel No idea. 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
[gmx-users] missing of methyl at N-terminal
hello everyone, for doing peptide with usual amino acid simulation. i m bringing my *.pdb file from insightII as i dont know any other tool or software from where i can get any pdb file (model peptide-Eg. Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by using pdb2gmx. it give error that no C is present at 6 NH2 position. tell me what to do. either tell me the name of free software or tool from where i can get the pdb of model peptide. tell me one more thing that whether gromacs only take those pdb's which are converted by babel Please help me out ___ 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
