[gmx-users] current directory files
tarak20489 at gmail.com
Fri Jun 15 10:21:04 CEST 2012
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 .....
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.Abraham at anu.edu.au>wrote:
> On 15/06/2012 4:27 PM, tarak karmakar wrote:
> Dear All,
> In my protein pdb file I have changed some of the amino acid residue
> names. So accordingly I have changed corresponding residue names in force
> filed files and kept all the files [ modified and unmodified ] in my
> current working directory. Those files are
> 1) atomtypes.atp
> 2) aminoacids.rtp
> 3) ffnonbonded.itp
> 4) ffbonded.itp
> 5) spc.itp
> 6) ions.itp
> now while giving the command
> pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top
> how can I make use of all these force field files present in my current
> working directory ?
> You need the kind of approach described here
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