AMBER Archive (2004)

Subject: RE: AMBER: can MM-PBSA be applied to Charmm format trajectory file?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 19 2004 - 14:02:50 CDT

Dear Jeny,

My experience with MM-PBSA is limited so I don't know if it can use a charmm
format trajectory. However, you can use ptraj to convert a charmm trajectory
to an amber one. Here is the ptraj input file you need:

trajin filename.charmm.crd
trajout filename.amber.crd trajectory

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of jz7_at_duke.edu
> Sent: 19 August 2004 11:55
> To: amber_at_scripps.edu
> Subject: AMBER: can MM-PBSA be applied to Charmm format
> trajectory file?
>
> Dear all,
>
> I wanted to estimate binding free energy for my protein-DNA system. It
> seems that the MM-PBSA program under Amber can do that. But
> the trajectory
> and other files I have are from NAMD (Charmm format). So I am
> wondering
> can MM-PBSA still work in this case? If not, is there any
> other program or
> method can estimate the protein-DNA binding free energy?
>
> Thanks a lot!
>
> Best,
> Jeny
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