AMBER Archive (2008)

Subject: Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jun 02 2008 - 14:11:24 CDT

those aren't mdcrd messages, they are for the prmtop.
can you send us your ptraj script?

On Mon, Jun 2, 2008 at 2:26 PM, Campbell, Patrick <pcampbell_at_msm.edu> wrote:
>
> Hello All,
>
> Following on the advice of Drs. Ross and Ibrahim, I ran a trajin analysis in
> ptraj to check the mdcrd file of my MD output ( I was getting difficulty
> generating slides for viewing in VMD - instead of a few thousand, I was only
> getting 12 slides from a 10 ns MD run).
>
> The following error messages came up with the analysis
>
>
>
> Error scanning a value: pert, ictper
> Dihedrals..
>
> Error scanning a value: pert, icpper
> Extra perturbation information...
>
> Error scanning a value: pert, iacper
> Successfully completed readParm.
>
> Initializing state: detected PBC beta angle in prmtop that is not 90.0!
> PTRAJ: Processing input file...
> Input is from standard input
>
> It would appear that there are some errors with the mdcrd file.
>
> I would appreciate any suggestions as to how I should proceed from this
> point. Ultimately, I would like to have a fully generated movie from the
> mdcrd file.
>
>
> Thanks again for all your hellp and do have a great day!
>
> Pat
>
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