AMBER Archive (2003)

Subject: Re: Ptraj problem with small molecules

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 04 2003 - 09:20:54 CST

On Tue, Feb 04, 2003, Dvira Segal wrote:
>
> I am still having problems loading topology files of small
> molecules in ptraj (amber7), even after i changed rdparm.c and recompiled
> the package.
> When Im running ptraj on methane, for example, I get the following message
>
> ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN
>
> when i try to load the topology file.
>
> any idea will be appreciated.
>
>
> By the way: Is anything missing in the patch (bugfix3), since there is a +
> on an empty line
>
> -----------------------------------------------------------
> *** rdparm.c 2001/10/02 21:44:46 1.12
> --- rdparm.c 2002/03/12 07:28:58 1.13
> ***************
> *** 1647,1654 ****
> --- 1647,1656 ----
> } /* END of: if ( parm->IFPERT ) */
>
> if (parm->JPARM == 1) {
> +
> fprintf(stderr, "Reading in LES information...\n");
>
> + if( newparm ) find_flag( parm->fp, "LES_NTYP" );
> parm->nlestyp = loadAndReturn12I6(parm->fp, 1, "LES, nlestyp");
> loadAndReturn12I6(parm->fp, 0, "");
>
>
> ---------------------------------------------------
>

Did you just apply the above patch? That has nothing to do with the problem
you are seeing. I think you have to go to Tom Cheatham's web site to get
the updates that fix your problem:

      http://www.chpc.utah.edu/~cheatham

Workaround is to just use the old format: "set default oldPrmtopFormat on"
in LEaP.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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