AMBER Archive (2002)

Subject: Re: Cap-atom-pointer in GIBBS

From: James W. Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Thu Dec 05 2002 - 13:23:45 CST

Once again...what version of amber are you using????

On Thu, 5 Dec 2002, Jose Ramon Blas wrote:

>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 |
> 

-- 

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James W. Caldwell                         (voice) 415-476-8603
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