Okay, thanks for the advice and apologies for my ignorance.
Regards,
Abhijeet
On Thu, Nov 17, 2016 at 8:14 PM, Nhai <nhai.qn.gmail.com> wrote:
> Ambertools 16 is free. Please use it, there are lots of enhancements
>
> Hai
>
> > On Nov 17, 2016, at 9:39 AM, ABHIJEET CHOWDHURY <
> f2013854.pilani.bits-pilani.ac.in> wrote:
> >
> > Dear David,
> >
> > Thank you for the information. Yes, indeed I am using AMBER 10 and so
> this
> > might be the case. Is there any other way to create a pdb format other
> than
> > using a newer version of AMBER.
> >
> > Regards,
> > Abhijeet
> >
> > On Thu, Nov 17, 2016 at 7:15 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >>> On Thu, Nov 17, 2016, ABHIJEET CHOWDHURY wrote:
> >>>
> >>> I want to convert my coordinate file generated into pdb format for
> >>> nuparm but unable to find the right tool. I tried using ptraj but was
> >>> unsuccessful. Although it created a pdb format but nuparm dose not
> >>> accepts it as .pdb.
> >>
> >> Use cpptraj or ambpdb from AmberTools16: these adhere more closely to
> >> the standard PDB format than does the (very old) ptraj program. Use the
> >> -bres flag to have residue names in the output PDB file match those in
> PDB
> >> standard.
> >>
> >> [Note: this may not work, since it looks(?) like you created the Amber
> >> files
> >> with an old version of the program that still used residue names like
> "RA"
> >> for
> >> adenosine (rather than the correct "A"). If ambpdb with the -bres flag
> >> doesn't make the name "A", you will have to edit the files to make that
> >> change
> >> yourself.]
> >>
> >> ...dac
> >>
> >>
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Received on Thu Nov 17 2016 - 07:00:03 PST
