[gmx-users] Dipeptide generation problem [Justin, Mark, Osmair]
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 26 20:46:17 CEST 2010
Eudes Fileti wrote:
> 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!
>
Probably nothing as smart as you need. The main problem was that you had (in
your original files) inconsistent numbering (multiple residue names as 1, then
2, then back to 1) and inconsistent names. If you have a dipeptide of Phe-Phe,
you don't have Lys and Asp at all, you just have termini, which are easily dealt
with in Gromacs if they are simply part of the Phe residue and are given the
correct atom names.
-Justin
>
> 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.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>
> Subject: Re: [gmx-users] Dipeptide generation problem [Justin]
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <fb1e9eeeeb59.4c772156 at anu.edu.au
> <mailto:fb1e9eeeeb59.4c772156 at anu.edu.au>>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> ----- Original Message -----
> From: Eudes Fileti <fileti at ufabc.edu.br <mailto:fileti at ufabc.edu.br>>
> Date: Friday, August 27, 2010 2:15
> Subject: Re: [gmx-users] Dipeptide generation problem [Justin]
> To: gmx-users at gromacs.org <mailto:gmx-users at 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
>
>
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> ------------------------------
>
> Message: 3
> Date: Thu, 26 Aug 2010 16:36:23 +0000
> From: Osmair Oliveira <osmair07 at hotmail.com
> <mailto:osmair07 at hotmail.com>>
> Subject: RE: [gmx-users] Dipeptide generation problem [Justin]
> To: <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID: <SNT110-W61A3EA483256A7CAF02DECC3850 at 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: fileti at ufabc.edu.br <mailto:fileti at ufabc.edu.br>
> To: gmx-users at gromacs.org <mailto:gmx-users at 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 <fileti at ufabc.edu.br <mailto:fileti at ufabc.edu.br>>
>
> Subject: [gmx-users] Dipeptide generation problem
>
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>
> Message-ID:
>
> <AANLkTikWxuC1g8fQ=fqnPfiXSWaDSTsPha=9QjPTDY38 at mail.gmail.com
> <mailto:9QjPTDY38 at 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
>
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> ------------------------------
>
>
>
> Message: 3
>
> Date: Thu, 26 Aug 2010 08:36:24 -0400
>
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
> Subject: Re: [gmx-users] Dipeptide generation problem
>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
> Message-ID: <4C765FC8.4020306 at vt.edu <mailto:4C765FC8.4020306 at 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 <http://vt.edu> | (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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
========================================
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