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.
Sincerely,
Shima
- Original Message -
From: Tsjerk Wassenaar tsje...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
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.
Cheers,
Tsjerk
On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh
shima_arasteh2...@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
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