What' in the bottom of drgcns.top?
On 9/6/2007 2:03 AM, Yafei Dai wrote:
Hi, all,
I am a new user of gromacs and I read the manual and tutorial but I still get
confused.
I need your help.
>From PRODRG, I got four *.top files, one *.itp file and three *.PDB files and some other files. In my system, I don't have any solvents, no any waters and no any ion.
I take the "DRGCNS.TOP : CNS topology file" and "DRGGMX.ITP : GROMACS .itp file" and
"DRGFIN.GRO : final coordinates in GROMOS87 format" to gromacs and do "grompp -v", but I get error
as below shows:
Fatal error: number of coordinates in coordinate file (drgfin.gro, 15)
does not match topology (drgcns.top, 0)
what can I do now? Thank you for you help.
yafei
----- Original Message -----
From: Yang Ye <[EMAIL PROTECTED]>
Date: Wednesday, September 5, 2007 2:24 am
Subject: Re: [gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?
Hi,
You need to get the topology file from PRODRG together with the
PDB file
so you skip pdb2gmx and use the outputs from PRODRG in grompp
directly.
Of cource, do whatever you need to add water and ions before grompp.
Regards,
Yang Ye
On 9/5/2007 10:51 AM, Yafei Dai wrote:
I got a pdb file from prodrg2 and I did pdb2gmx:
pdb2gmx -f test.pdb -p test.top -o test.gro
I was told "DRG" not found in residue topology. What can I do
for this error information? My pdb file is as below:
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