Hi Eudes, I do not know how work CHARMM force field, but if you use the following PDB file for your dipeptide using OPLS-AA force field, you can obtain good results!.
ATOM 1 N PHE 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 H1 PHE 1 -0.940 0.000 -0.330 1.00 0.00 ATOM 3 H2 PHE 1 0.470 0.820 -0.330 1.00 0.00 ATOM 4 H3 PHE 1 0.470 -0.820 -0.330 1.00 0.00 ATOM 5 CA PHE 1 0.000 0.000 1.460 1.00 0.00 ATOM 6 HA PHE 1 -0.500 0.920 1.790 1.00 0.00 ATOM 7 CB PHE 1 -0.780 -1.200 1.990 1.00 0.00 ATOM 8 HB1 PHE 1 -0.340 -2.120 1.570 1.00 0.00 ATOM 9 HB2 PHE 1 -0.670 -1.250 3.080 1.00 0.00 ATOM 10 CG PHE 1 -2.240 -1.170 1.650 1.00 0.00 ATOM 11 CD1 PHE 1 -3.140 -0.480 2.450 1.00 0.00 ATOM 12 HD1 PHE 1 -2.770 0.040 3.340 1.00 0.00 ATOM 13 CD2 PHE 1 -2.730 -1.830 0.530 1.00 0.00 ATOM 14 HD2 PHE 1 -2.030 -2.380 -0.120 1.00 0.00 ATOM 15 CE1 PHE 1 -4.490 -0.450 2.140 1.00 0.00 ATOM 16 HE1 PHE 1 -5.180 0.100 2.790 1.00 0.00 ATOM 17 CE2 PHE 1 -4.070 -1.800 0.220 1.00 0.00 ATOM 18 HE2 PHE 1 -4.440 -2.330 -0.670 1.00 0.00 ATOM 19 CZ PHE 1 -4.950 -1.110 1.020 1.00 0.00 ATOM 20 HZ PHE 1 -6.020 -1.090 0.780 1.00 0.00 ATOM 21 C PHE 1 1.400 0.000 2.020 1.00 0.00 ATOM 22 O PHE 1 2.160 -0.950 1.880 1.00 0.00 ATOM 23 N PHE 2 1.710 1.140 2.660 1.00 0.00 ATOM 24 H PHE 2 0.990 1.860 2.700 1.00 0.00 ATOM 25 CA PHE 2 3.020 1.330 3.260 1.00 0.00 ATOM 26 HA PHE 2 3.770 1.260 2.460 1.00 0.00 ATOM 27 CB PHE 2 3.100 2.720 3.900 1.00 0.00 ATOM 28 HB1 PHE 2 2.290 2.820 4.630 1.00 0.00 ATOM 29 HB2 PHE 2 4.050 2.800 4.460 1.00 0.00 ATOM 30 CG PHE 2 3.020 3.850 2.920 1.00 0.00 ATOM 31 CD1 PHE 2 4.150 4.290 2.250 1.00 0.00 ATOM 32 HD1 PHE 2 5.120 3.820 2.450 1.00 0.00 ATOM 33 CD2 PHE 2 1.810 4.460 2.650 1.00 0.00 ATOM 34 HD2 PHE 2 0.900 4.120 3.160 1.00 0.00 ATOM 35 CE1 PHE 2 4.070 5.330 1.340 1.00 0.00 ATOM 36 HE1 PHE 2 4.980 5.670 0.830 1.00 0.00 ATOM 37 CE2 PHE 2 1.730 5.500 1.740 1.00 0.00 ATOM 38 HE2 PHE 2 0.760 5.980 1.540 1.00 0.00 ATOM 39 CZ PHE 2 2.860 5.940 1.090 1.00 0.00 ATOM 40 HZ PHE 2 2.800 6.760 0.360 1.00 0.00 ATOM 41 C PHE 2 3.320 0.260 4.290 1.00 0.00 ATOM 42 O1 PHE 2 2.370 -0.690 4.490 1.00 0.00 ATOM 43 O2 PHE 2 4.520 0.340 4.920 1.00 0.00 By Osmair Federal University of Sao Carlos - Brazil Date: Thu, 26 Aug 2010 13:14:20 -0300 Subject: Re: [gmx-users] Dipeptide generation problem [Justin] From: fil...@ufabc.edu.br To: gmx-users@gromacs.org Olá Justin, thank you for responding to my post. I had tried what you mentioned before. All I get is that the some atoms are missing (see error message in the link https://sites.google.com/site/fileti/ ). In fact, as I just want NH3+ (from LYS) and COO- (from ASP), the other atoms are not included in PDB file and this can give error. If I put everything into the same group ("1" for example) many of the atoms are deleted by pdb2gmx because they are duplicates. In fact I still do not quite understand the logic of creating a PDB from the aminoacid residues. I've read some tips on the list but still I could not understand. That's it. If you have any suggestion, it will be very useful. Até maiseef_______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br ------------------------------ Message: 2 Date: Thu, 26 Aug 2010 09:32:06 -0300 From: Eudes Fileti <fil...@ufabc.edu.br> Subject: [gmx-users] Dipeptide generation problem To: gmx-users@gromacs.org Message-ID: <aanlktikwxuc1g8fq=fqnpfixswadstspha=9qjptd...@mail.gmail.com> Content-Type: text/plain; charset="windows-1252" Hello everybody, I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. This dipeptide has a positively charged site (NH3+) and a negatively charged site (COO-). My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be consistent and produces error when I execute pdb2gmx. The link above presents the PDB and the error message from pdb2gmx (which I have not found similar in the forum). Could someone give me a hand with that? Bests eef _______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html ------------------------------ Message: 3 Date: Thu, 26 Aug 2010 08:36:24 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] Dipeptide generation problem To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4c765fc8.4020...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Eudes Fileti wrote: > Hello everybody, > I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. > This dipeptide has a positively charged site (NH3+) and a negatively > charged site (COO-). > My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to > be consistent > and produces error when I execute pdb2gmx. > > The link above presents the PDB and the error message from pdb2gmx > (which I have not found similar in the forum). > > Could someone give me a hand with that? > Your .pdb file contains various broken residues (ASP, LYS) and non-sequential numbering (i.e., those broken residues are all numbered 1). Clean up the .pdb and try again. -Justin > Bests > eef > _______________________________________ > Eudes Eterno Fileti > Centro de Ciências Naturais e Humanas > Universidade Federal do ABC — CCNH > Av. dos Estados, 5001 > Santo André - SP - Brasil > CEP 09210-971 > +55.11.4996-0196 > http://fileti.ufabc.edu.br > -- ======================================== 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
-- 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