AMBER Archive (2002)

Subject: Cap-atom-pointer in GIBBS

From: Jose Ramon Blas (jramon_at_ub222059.pcb.ub.es)
Date: Thu Dec 05 2002 - 13:50:45 CST

Hi, when I set in GIBBS input:
ivcap=1, natcap=5697, fcap=3.0,isolvp=5697,
...I expect PARM-cap-atom-pointer (if any) to be overwritten by 5697.

But what I find in GIBBS output file is:
 %GIBBS-I-CAPMOD, cap parameters modified

     IVCAP = 1 MATCAP= 0 IFCAP = 0
     NATCAP= 0 CUTCAP= 0.00000

     XCAP = 0.00000 YCAP = 0.00000
     ZCAP = 0.00000 FCAP = 3.00000
...and some lines later...
 Solute/solvent pointers:
     IPTSOL= 3730 NATRCM=15798
     IPTRES= 0 IPTATM= 0
     NSPSOL= 0 NSPSTR= 0
     NSOLUT= 5697 NATOM =1579

>From here I deduce that the progam perfectly distinguishes between what is
solvent/solute (NSOLUT= 5697), but it fails when expressing in the output
what it has read from the input (natcap=5697 --> NATCAP= 0). This would
have NO EFFECT on gibbs run.
Is this interpretation right??

Thanks a lot for the answers,

Jose Ramon

---------------------------------------------------------------------------
Jose R. Blas
Molecular Modelling & Bioinformatics
IRBB, Parc Cientific de Barcelona |e-mail:jramon_at_mmb.pcb.ub.es
C/Josep Samitier 1-5, | phone: + 34 93 40371 55
08028 Barcelona |