AMBER Archive (2002)

Subject: carnal and union

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Mon Mar 04 2002 - 03:00:20 CST


Hi,

I would like to calculate hydrogen bonds (occupancy) between a ligand, a
protein and the water molecules (more than 10 000).

As the number of water molecules is very big, I always obtain a swap
memory error. So I decided to select several water molecules.

In my carnal input file, I wrote:
 
DECLARE
 GROUP g1 (RES 389);
 GROUP g2 (ATOM TYPE OW);
 GROUP g31 (RES 37,38,53,55,68-71,75,97-100,114-118,121,
141-147,162-170);
 GROUP g32 (RES 194-197,212-215,265-269,290,323-324,345,347,351,359);
 GROUP g3 (g31 | g32);
 GROUP g41 (RES 395-398, 403-408,417,430, 436);
 GROUP g42 (RES 456-457, 473, 476, 484, 506, 548-549);
 GROUP g43 (RES 578-584, 597-598, 218, 220, 228, 508-509);
 GROUP g4 (g41 | g42 | g43)
OUTPUT
 HBOND h1 DONOR g1 ACCEPTOR g2 STATS;
 HBOND h2 DONOR g2 ACCEPTOR g1 STATS;
 HBOND h3 DONOR g1 ACCEPTOR g3 STATS;
 HBOND h4 DONOR g3 ACCEPTOR g1 STATS;
 HBOND h5 DONOR g3 ACCEPTOR g4 STATS;
 HBOND h6 DONOR g4 ACCEPTOR g3 STATS;
END

I always obtain an error at this line :
 GROUP g3 (g31 | g32); where I want to group together group g31 and the
group g32 to obtain one group g3.

How I can do that, please?

Thanks
pascal.

-- 
***************************************************
 Dr. Pascal Bonnet
 School of Pharmacy and Pharmaceutical Sciences,
 University of Manchester, Manchester, M13 9PL, U.K.
 Tel:(+44) (0)161 275 2431
 http://www.man.ac.uk/~mbpsspb3