Generally I am using this command in tleap to do this job.
source leaprc.ff99bsc0
WAT = SPC
mod0 = loadAmberParams frcmod.spce
set WAT.1 name "SPC"
mypdb = loadpdb pack.pdb
check mypdb
charge mypdb
savepdb .pdb
saveAmberParm mypdb packpdb.top packpdb.crd
quit
Remember advice of Prof. Case about PDB format.
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
On Thu, Sep 1, 2016 at 3:24 AM, Budhathoki, Dipesh <
budhdipe.pharmacy.isu.edu> wrote:
> Thank you for this quick response and I was able to do that. Actually, even
> I was surprised when my instructor first told me to do that. Now, I don't
> know why I am doing this!!
>
> On Wed, Aug 31, 2016 at 2:38 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Wed, Aug 31, 2016, Adrian Roitberg wrote:
> >
> > > It is not clear to me WHY you want to do what you want to do, but
> > > anyways, you need to do
> > >
> > > sed 's/HOH /TIP3P/g' filename
> > >
> > > Note space after HOH. That way you will replace a 4 character string
> > > with a 4 character string and the rest should stay the same.
> >
> > Idea is OK, but actual character count is suspect :-)
> >
> > Note that the PDB format only allows three characters for the residue
> name
> > (columns 18-20).
> >
> > ...dac
> >
> >
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> >
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Received on Wed Aug 31 2016 - 22:00:02 PDT
