Re: AMBER: rmsd calculation in ptraj

From: Carlos Simmerling <>
Date: Sat, 10 Mar 2007 09:26:34 -0500

it would help if you show us the real ptraj input.
in particular, you aren't really saying":mask" for the mask, are you?

On 3/10/07, gurpreet singh <> wrote:
> hello amber users
> i m using ptraj module of amber9 to calculate the rmsd( backbone only) over
> the whole trajectory of the simulation taking the crystal structure as the
> reference and i m getting values in the range of 35 to 38 although there is
> no significant change in the structure during the simulation. To verify
> the results i calculated the rmsd of the individual structure using VMD and
> their the rmsd is coming fine as expected.
> the command which i used in ptraj was:
> strip :WAT
> reference my crystal structure.pdb
> rms reference out rmsbackbone.dat :mask
> if the problem is in the input then please tell me the suitable
> corrections i need to make and if not suggest some other ways by which i
> can rectify the problem
> thanks
> Gurpreet Singh
> MS
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Received on Sun Mar 11 2007 - 06:07:37 PDT
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