Re: [AMBER] Converting coordinate file generated into pdb format for nuparm

Date: Thu, 17 Nov 2016 20:09:02 +0530

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.


On Thu, Nov 17, 2016 at 7:15 PM, David A Case <>

> 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 - 07:00:02 PST
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