AMBER Archive (2002)

Subject: Chains, LEaP and ambpdb

From: Luis Gracia (luis.gracia_at_mssm.edu)
Date: Tue Dec 17 2002 - 13:47:59 CST

Hi everybody!

I constructed a system with LEaP that has more than 10000 waters. When
converting the files to pdb with the program ambpdb I get **** in the
residue number from 10000 up. Does anyone know about a script to get
around this, may be adding chain labels every 10000 water molecules? I
also need to read a md simulation output from this system back in LEaP
again, and it seems to me that it is only possible converting the
restart file to pdb. Is there a way to input the amber restrt file into
LEaP?

Thank a lot, and happy holidays!

Best, Luis 

-- 
Luis Gracia, PhD
Dept. Physiology & Biophysics, 21-280
Mt Sinai School of Medicine
One Gustave L. Levy Place, New York NY 10029
Tel: (212) 241-0858   ---   Fax: (212) 860-3369
e.mail: luis.gracia_at_mssm.edu