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.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Subject: Re: [gmx-users] Dipeptide generation problem [Justin]
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <fb1e9eeeeb59.4c772...@anu.edu.au
<mailto:fb1e9eeeeb59.4c772...@anu.edu.au>>
Content-Type: text/plain; charset="iso-8859-1"
----- Original Message -----
From: Eudes Fileti <fil...@ufabc.edu.br <mailto:fil...@ufabc.edu.br>>
Date: Friday, August 27, 2010 2:15
Subject: Re: [gmx-users] Dipeptide generation problem [Justin]
To: gmx-users@gromacs.org <mailto: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
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Message: 3
Date: Thu, 26 Aug 2010 16:36:23 +0000
From: Osmair Oliveira <osmai...@hotmail.com
<mailto:osmai...@hotmail.com>>
Subject: RE: [gmx-users] Dipeptide generation problem [Justin]
To: <gmx-users@gromacs.org <mailto: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 <mailto:fil...@ufabc.edu.br>
To: gmx-users@gromacs.org <mailto: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 <mailto:fil...@ufabc.edu.br>>
Subject: [gmx-users] Dipeptide generation problem
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<aanlktikwxuc1g8fq=fqnpfixswadstspha=9qjptd...@mail.gmail.com
<mailto: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
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Message: 3
Date: Thu, 26 Aug 2010 08:36:24 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Dipeptide generation problem
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4c765fc8.4020...@vt.edu <mailto: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 <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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