On 15/06/2012 6:21 PM, tarak karmakar wrote:
Hi,
Thanks for the reply.
One thing, while giving the '-ff' flag it is asking for some string.
So I renamed all my force field files as except spc.itp and ions.itp.
Renamed files are .....
1) ffprot.atp
2) ffprot.rtp
3) ffprot.itp [ includes ffnonbonded.itp and ffbonded.itp ]
pdb2gmx -f test.pdb -o test.gro -p toplo.top -ff prot
so it'll read all of these files starting with 'ff'
Then how can I deal with spc.itp and ions.itp files ?? Should I
include the scp.itp and ions.itp files inside the ffprot,itp ??
On Fri, Jun 15, 2012 at 12:50 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
You need the kind of approach described here
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
You started with files from some force field. Copy the whole folder,
like it says in the above link. Then modify the files there...
Mark
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