AMBER Archive (2007)

Subject: Re: AMBER: radius of gyration

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Mon Jan 29 2007 - 09:51:26 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.
 
 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).
 
 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
>
>
>
> Esther B.
>
>
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Esther B.

 
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