AMBER Archive (2003)

Subject: Predefined Water_cap with xleap

From: Jose Ramon Blas (jramon_at_ub222059.pcb.ub.es)
Date: Wed Jan 08 2003 - 12:42:16 CST

Hi,
I have coordinates for a protein surrounded by counterions and a SOLVENT
drop (solvent is heterogeneous --not only one type of residue--).

I load this in xleap (loadpdb), but I want that the generated unit when
saved as a topology, clearly distingishes between SOLUTE/SOLVENT parts. Is
this possible with xleap?? Because if, when running gibbs, I make use of
the ivcap & natcap & fcap keywords in order to apply the common
cap-restraint , things do not work properly and solvent evaporates!!

Thanks for any help,

Jose Ramon

---------------------------------------------------------------------------
Jose R. Blas
Molecular Modelling & Bioinformatics e-mail: jramon_at_mmb.pcb.ub.es
IRBB, Parc Cientific de Barcelona phone: + 34 93 403 71 55
C/Josep Samitier 1-5,
08028 Barcelona