Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 13 Oct 2014 21:02:29 -0400

On Mon, Oct 13, 2014, Hirdesh Kumar wrote:

> ambpdb -p complex.prmtop <eq5.rst> eq5.pdb
> | New format PARM file being parsed.
> | Version = 1.000 Date = 10/13/14 Time = 15:39:06
>
> ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0
>
>
> but when I use this script
> pdb.in:
> trajin eq5.rst 1 1 1
> trajout try1.pdb pdb
>
> cpptraj complex.prmtop pdb.in => I get the pdb file.
>
> Is it because of ioutfm=1, ntxo=2 in my input files?

Yes: ambpdb only knows about formatted restart files. I think Dan has a
script that emulates the ambpdb functionality, but actually runs things
through cpptraj. It's probably time to get that out to users.

....dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 13 2014 - 18:30:02 PDT
Custom Search