AMBER Archive (2007)

Subject: Re: AMBER: radius of gyration

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jan 29 2007 - 13:51:39 CST

> Thanks for your help! I check the AMBER archive files, it seems Ptraj
> (AMBER8) can't calcuate the radius of gyration, am I right? Only Amber
> 9 can.

I think you can download more recent versions of ptraj?

> Also I want to calcuate the distance between the specified atom to the
>center of the mass of the molecue, Ptraj in Amber 8 can do that? I found
>Carnal can do it, but I didn't know how to do it with Ptraj (Amber8).

These are all questions for the author of ptraj, Tom Cheatham.

Bill

>
> Thanks a lot for your help!
> Bests,
>
> Bill Ross <ross_at_cgl.ucsf.edu> wrote: > Internal error: stream file name 2 out of range
>
> Your input looks correct and the size of the mdcrd file shouldn't
> be an issue. If the measurements look reasonable I think all is ok.
> The error msg implies that carnal thinks there is a second input
> file. Since carnal isn't supported any more, you might want to
> replicate the result with ptraj.
>
> Bill
>
> > Dear ALL,
> >
> > I am trying to calculate the radius of gyration by Carnal (AMBER8).
> > I want to measure it through my md trajactory mdcrd file.
> > Here is my simple input Analin file:
> > FILES_IN
> > PARM p1 prmtop;
> > STREAM s1 mdcrd;
> > FILES_OUT
> > TABLE tab1 radgyr.tbl;
> > DECLARE
> > GROUP groupid1 (RES 1-5);
> > OUTPUT
> > TABLE tab1 groupid1%radgyr;
> > END
> >
> > But it shows errors in the output file, do you think it is because of my big mdcrd file? Thank you very much for your any advice!
> >
> > CARNAL -
> > AMBER 8.0
> >
> > COORDINATE ANALYSIS
> >
> >
> > input Analin
> > > FILES_IN
> > > PARM p1 prmtop;
> > Reading parm file (prmtop)
> > parm: opening prmtop
> > > STREAM s1 mdcrd;
> > Using default parm (prmtop) for STREAM s1
> > (box will be read from stream)
> > stream: opening mdcrd.
> > > FILES_OUT
> > > TABLE tab1 radgyr.tbl;
> > > DECLARE
> > > GROUP groupid1 (RES 1-5);
> > ** Group groupid1: 1340 atoms
> > > OUTPUT
> > > TABLE tab1 groupid1%radgyr;
> > > END
> > (EOF reached on mdcrd)
> > STREAM s1: no more files/crds (iteration 2500)
> > SUMMARY
> > (EOF reached on mdcrd)
> > Internal error: stream file name 2 out of range
> >
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