AMBER Archive (2009)

Subject: RE: [AMBER] CHARMM psf file to Amber prmtop file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 24 2009 - 17:11:36 CST

Dear Sarvin,

You do not say why you want to convert your dcd and psf file specifically to
a prmtop file. What exactly do you want to achieve here? If it is to be able
to run a CHARMM simulation in AMBER. I.e. to use PMEMD to run a simulation
using the CHARMM force field then you can do this with the program CHAMBER
which is part of AMBER Tools 1.3. See the manual on the amber webpage.

Make sure you have applied all the latest bugfixes to AMBER 10 before using
this prmtop.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Sarvin Moghaddam
> Sent: Wednesday, December 23, 2009 8:21 AM
> To: AMBER Mailing List
> Subject: [AMBER] CHARMM psf file to Amber prmtop file
>
> Hello All,
>
> I was wondering if somebody can help me with the following:
>
> I have CHARMM dcd and psf files and need to convert them to Amber xyz
> and prmtop files.
>
> I have extracted Cartesian coordinates from my CHARMM dcd file and I
> believe (haven't tried it yet) ptraj can convert that to Amber
> coordinates but was wondering
> if there is anyway to do convert the CHARMM psf to amber prmtop as
> well?
>
> I found the same query in Amber email list but couldn't find the answer
> and was hoping maybe "by now" somebody knows the trick?!
>
> Thanks in advance.
>
> Sarvin
>
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