AMBER Archive (2001)

Subject: TOPOLOGY FILE PROCESSING

From: Carles Ferrer (gandalf_at_husky.bq.ub.es)
Date: Thu Dec 20 2001 - 12:01:04 CST

Hi,
it is very easy in AMBER to dealt with trajectories (strip
atoms/residues,
strip snapshots, center,...) by using ptraj.
Removing atoms/residues from a topology file is not so automatic. As far
as
I know, rdparm only can remove solvent (if it is water) and it is not
so
automatic as ptraj to introduce it in a UNIX shell script. Is this true?

Does anyone know about any procedure to strip the desired atoms/residues
from a topology file that could be easily used on hundreds of topology
files
as ptraj does on trajectories?

Any suggestion is greatly appreciated,

Blas

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J.R. Blas
                    
Grup de RECONEIXEMENT MOLECULAR | e-mail:jramon_at_husky.bq.ub.es
Dept.Bioquimica i Biol.Molecular | phone: + 34 93 403 58 58
Facultat de Quimica | FAX: + 34 93 402 12 19
Universitat de Barcelona |
Marti i Franques,1 |
08028 Barcelona |