Olá, Justin, Mark and Osmair. Thanks for help. Building dipeptide has not been the problem. Actually I need to use atomic coordinates obtained from a previous X-ray crystal structure. For this, I need to give each atom its proper name. That is, I have this: ... ATOM 10 C UNK 1 -2.980 6.010 1.900 1.00 0.00
ATOM 11 C UNK 1 -2.380 5.770 1.130 1.00 0.00 ATOM 12 H UNK 1 -4.050 7.000 1.400 1.00 0.00 ATOM 13 H UNK 1 -3.590 7.740 0.930 1.00 0.00 ATOM 14 H UNK 1 -4.620 6.540 0.740 1.00 0.00 ATOM 15 C UNK 1 -4.930 7.590 2.470 1.00 0.00 ... and I need something like this: ... ATOM 10 CG PHE 1 -2.980 6.010 1.900 1.00 0.00 ATOM 11 CD1 PHE 1 -2.380 5.770 1.130 1.00 0.00 ATOM 12 HD1 PHE 1 -4.050 7.000 1.400 1.00 0.00 ATOM 13 CD2 PHE 1 -3.590 7.740 0.930 1.00 0.00 ATOM 14 HD2 PHE 1 -4.620 6.540 0.740 1.00 0.00 ATOM 15 CE1 PHE 1 -4.930 7.590 2.470 1.00 0.00 ... Of course if I try to use pdb2gmx without assigning these names, the execution fails. I know this should be simple and that there should be several ways to revolve, but it's puzzling me. Is there any software or script I can use to do that automatically? Any hint is very welcome! Até mais 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 From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Dipeptide generation problem [Justin] > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <fb1e9eeeeb59.4c772...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > > > ----- Original Message ----- > From: Eudes Fileti <fil...@ufabc.edu.br> > Date: Friday, August 27, 2010 2:15 > Subject: Re: [gmx-users] Dipeptide generation problem [Justin] > 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. > > Have a look some MD tutorial material (doesn't have to be GROMACS). They > probably start with a well-formed PDB file. That's probably a better > learning experience than trying to read the format description. > > Alternatively, use a molecule builder (search webpage for suggestions here) > to create the coordinates, and then get pdb2gmx to do the rest of the work. > > The idea behind pdb2gmx is that you don't have to move mountains to get > your termini right, and the corresponding topology. If you just give it two > adjacent PHE (charged or not), you can tell pdb2gmx what termini you want it > to have. Done right, this whole task should not require you to inspect or > change a coordinate file at all. > > Mark > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100827/543767bc/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 26 Aug 2010 16:36:23 +0000 > From: Osmair Oliveira <osmai...@hotmail.com> > Subject: RE: [gmx-users] Dipeptide generation problem [Justin] > To: <gmx-users@gromacs.org> > Message-ID: <snt110-w61a3ea483256a7caf02decc3...@phx.gbl> > Content-Type: text/plain; charset="windows-1252" > > > 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 > > > > ======================================== > > > > --
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