AMBER Archive (2004)

Subject: Re: AMBER: some bugfixes

From: David A. Case (case_at_scripps.edu)
Date: Mon May 10 2004 - 18:10:08 CDT

On Mon, May 03, 2004, Sbastien Osborne wrote:

> Another bug to tell you... Gibbs does not read CUTCAP, XCAP, YCAP and
> ZCAP from the topology file, which causes gibbs simulation with solvent
> cap to crash because the center of the cap is set at 0.0 with a 0
> radius. Found that out the hard way ;)
>

Thanks for the report. Here is patch (untested, but compiles) that looks
like it should fix this problem:

*** giba.f 2002/01/30 00:34:33 7.14
--- giba.f 2004/05/10 23:00:59
***************
*** 306,311 ****
--- 306,326 ----
          TYPE = 'CAP_INFO'
          CALL NXTSEC(NF, 6, 1,FMTIN, TYPE, FMT, IOK)
          READ(NF,FMT) NATCAP
+ c
+ FMTIN = '(4E16.8)'
+ TYPE = 'CAP_INFO2'
+ CALL NXTSEC(NF, 6, 0,FMTIN, TYPE, FMT, IOK)
+ READ(NF,FMT) CUTCAP,XCAP,YCAP,ZCAP
+ c
+ write(6,8128) natcap,cutcap,xcap,ycap,zcap
+ 8128 format(t2,'cap option on:',
+ $ /,'NATCAP = ',I5,' CUTCAP = ',F10.3,' XYZCAP = ',3F8.3)
+ ELSE
+ NATCAP = 0
+ CUTCAP = 0.0D0
+ XCAP = 0.0D0
+ YCAP = 0.0D0
+ ZCAP = 0.0D0
        END IF
  C
  C ----- LOAD THE INFORMATION FOR PERTURBATION -----

This should work with either Amber7 or Amber8. (You may have already
done this yourself....).

As you can tell, few people on the Amber list still use gibbs, so our ability
to offer advice is limited. But we will try to to what we can, including
fixing bugs. (The above problem was introduced when converting gibbs to
read the "new" format prmtop files. Apparently, no test calculations with the
"cap" option were ever carried out....)

Thanks again for your input....regards...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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