VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 27 2006 - 13:56:03 CST
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Hi,
It sounds like you're running APBS 0.4.x, which has the new 'sdens'
config file requirement compared with the older versions.
The beta versions of VMD 1.8.4 have already been updated with the latest
APBS plugin which emits config files containing the "sdens" keyword which
should solve your problem: http://www.ks.uiuc.edu/Research/vmd/alpha/
John Stone
vmd_at_ks.uiuc.edu
On Thu, Jan 26, 2006 at 08:38:15PM -0600, Zhiyong Zhang wrote:
> Dear VMD users,
>
> I met a problem when I used APBS plugin in VMD 1.8.4a22 (under LINUX).
> After I clicked 'Run APBS', the pot.dx was not generated although there
> is an apbs.in file under the directory. I then used this input file to
> run apbs directly:
>
> ./apbs apbs.in, but there is an error:
>
> Parsing input file apbs.in...
> PBEparm_check: SDENS not set!
> NOsh: MG parameters not set correctly!
> Error while parsing input file.
>
> I had to modify the apbs.in, and set the parameter 'sdens' by myself.
> After that, there is no problem to run: ./apbs apbs.in
>
> It seems that the apbs.in file generated by VMD plugin miss the
> parameter 'sdens'. I am wondering if anybody met this problem before,
> please advise.
>
> Thanks,
> Zhiyong Zhang
> --
> Postdoctoral Fellow,
> School of Health Information Sciences,
> University of Texas Health Science Center - Houston,
> 7000 Fannin St., suite 1480,
> Houston, TX 77030, U.S.A.
> email: Zhiyong.Zhang_at_uth.tmc.edu
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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