[gmx-users] Output of rotation

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Sep 30 11:42:10 CEST 2012

The input file has TER  between 2 monomers. 
The command which I use is:
#editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro

After that, I use editconf to convert .gro to .pdb file:
#editconf -f protein-rotate.gro -o protein.pdb

The residue numbers after 10th one of output pdb file are changed and not correct. 


----- Original Message -----
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, September 30, 2012 12:17 PM
Subject: Re: [gmx-users] Output of rotation

Hi Shima,

How did you rotate the structure? Probably the TER records got lost in
the process.



On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh
<shima_arasteh2001 at yahoo.com> wrote:
> Dear gmx users,
> I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect.
> The pdb file was visualized and its format seems to be correct.
> Anybody knows what is the problem? How can I overcome this problem?
> Please help me
> Thanks in advance.
> Sincerely,
> Shima
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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