[gmx-users] Dipeptide generation problem [Justin, Mark, Osmair]
Eudes Fileti
fileti at ufabc.edu.br
Thu Aug 26 20:41:44 CEST 2010
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.abraham at anu.edu.au>
> Subject: Re: [gmx-users] Dipeptide generation problem [Justin]
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fb1e9eeeeb59.4c772156 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> ----- Original Message -----
> From: Eudes Fileti <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
>
> > 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 <osmair07 at hotmail.com>
> Subject: RE: [gmx-users] Dipeptide generation problem [Justin]
> To: <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
> To: 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>
>
> Subject: [gmx-users] Dipeptide generation problem
>
> To: gmx-users at gromacs.org
>
> Message-ID:
>
> <AANLkTikWxuC1g8fQ=fqnPfiXSWaDSTsPha=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
>
> -------------- 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" <jalemkul at vt.edu>
>
> Subject: Re: [gmx-users] Dipeptide generation problem
>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> Message-ID: <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 | (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
> ========================================
>
>
>
> --
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100826/04420047/attachment.html>
More information about the gromacs.org_gmx-users
mailing list