AMBER Archive (2006)

Subject: Re: AMBER: ptraj vector

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Jun 20 2006 - 16:55:05 CDT

Thanks.

This is my input file.
I'm doing that also.

=======================
trajin md2.trj.gz 501
#trajin md3.trj.gz
#trajin md4.trj.gz
#trajin md5.trj.gz
#trajin md6.trj.gz
#trajin md7.trj.gz 1 500 1
vector v1 @12 @13
#vector v2 :4-37_at_P corrplane order 2
analyze timecorr vec1 v1 tcorr 1500 dplr norm out cn.cf
#analyze timecorr vec1 v2 tcorr 1500 out memb.cf
#analyze timecorr vec1 v1 vec2 v2 tcorr 1500 drct dplr norm out cn-memb.cf
go
=============================

Nothing works.

The warning message is

WARNING in ptraj(), analyze timecorr: wrong vector type given, ignoring command

As I have mentioned, vector problem can be solved by removing "corr",
but "analyze timecorr" never works.

On 6/20/06, David A. Case <case_at_scripps.edu> wrote:
> On Tue, Jun 20, 2006, Myunggi Yi wrote:
> >
> > I have tried the followings, both didn't work.
> >
> > ==========================
> > vector v1 @12 [corr] @13
> > analyze timecorr vec1 v1 tcorr 2000 dplr out cn.cf
> > go
>
> Weird.. I use the "vector" command all the time, but I always use the
> ":2_at_N" type syntax, (i.e. residue number, atom name). It might be worth
> playing with alternatives in the atom-mask syntax -- at least you might get a
> different error message!
>
> ...just grasping at straws here....dac
>
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-- 
Best wishes,

MYUNGGI YI
==================================
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Institute of Molecular Biophysics
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