[gmx-users] Dipeptide generation problem [Justin]
Osmair Oliveira
osmair07 at hotmail.com
Thu Aug 26 18:36:23 CEST 2010
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
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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
========================================
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