AMBER Archive (2004)

Subject: Re: AMBER: ptraj

From: Holly Freedman (holly_at_mercury.hec.utah.edu)
Date: Tue May 25 2004 - 19:45:24 CDT

Ross,

I had been using AMBER7 and, ptraj could read the new topology file that
you made for me but the results look bad. I am trying to find radial
distribution functions from an md trajectory, and all of the computed
rdfs in the *_volume.xmgr are zero everywhere.
Thanks for your help,

-- Holly

Ross Walker wrote:

> Dear Holly,
>
> You don't say specifically what program you are using to read in your
> topology file and also what version of amber you are using. The
> topology file you attached is read fine by rdparm in amber 8. Can you
> read other topology files ok?
>
> I have converted this file to an Amber6 topology file for you using
> new2oldparm. Try this version of the parmtop file and see if you still
> get an error.
>
> If you do then can you please provide us with some more information.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
> ------------------------------------------------------------------------
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
> Behalf Of Holly Freedman
> Sent: 25 May 2004 09:17
> To: amber_at_scripps.edu
> Subject: AMBER: ptraj
>
> Hi,
>
> I am running ptraj on a trajectory generated for CH3Cl in water
> and am getting an error when trying to read the prmtop file, which
> I am attaching.
> The error says
>
> Read in info for bonds w/out hydrogen...
>
> ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN
>
> Does anyone know how to get around this bug?
> Thanks in advance for your help. If anyone knows how to modify
> this prmtop so that ptraj will read it, this would be so helpful
> to me.
>
> --Holly Freedman
> University of Utah
>

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