31 mar 2007 kl. 21.15 skrev özge kül:
Hi
My question was about my molecule has two chains and I at least
(after several analyze graphics)understood the chains are splitting
up and then get together when I watched the protein in VMD.The
chains get together with SS bonds.I read the manu
Specbond.dat is used to construct the topology, Ozge. so it is used by pdb2gmx
program.
Alpay
Message: 6
Date: Sat, 31 Mar 2007 00:36:14 +0200
From: Erik Marklund <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] splitting chains
To: Discussion list for GROMACS users
Message-ID: <[EMAIL
Tsjerk Wassenaar wrote:
Ozge,
We are, at least I am, getting the impression that you refuse to try
to think for your self. This makes trying to help you very
unsatisfactory. We are not here to do your homework.
Ok, that been said, I'll make it brief. You shouldn't need to edit the
specbond.dat
Ozge,
We are, at least I am, getting the impression that you refuse to try
to think for your self. This makes trying to help you very
unsatisfactory. We are not here to do your homework.
Ok, that been said, I'll make it brief. You shouldn't need to edit the
specbond.dat (in the gromacs topology/
30 mar 2007 kl. 22.40 skrev özge kül:
Hi Andrea,
This is my .top file
more 1ppbfree.top
;
; File '1ppbfree.top' was generated
; By user: ozge (502)
; On host: druggrid
; At date: Thu Mar 15 23:17:25 2007
;
; This is your topology file
; ALPHA-THROMBIN (E.C
30 mar 2007 kl. 22.32 skrev özge kül:
Hi Eric,
Where is the specbond.dat?After which line is it formed?
specbond.dat is located in /share/gromacs/top/
I don't understand the question about the line.
/Erik
1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o
1ppbfree.gro -merge
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