Subject: Re: CCL:PDB files: Adding (polar) H and atomic charges - free software?

From: "Nikos" <[email-masked]>
Date: Thu, 9 Mar 2000 17:09:52 +0200

Dear Eldbjørg ,
a solution to your problem might be downloading the free version of
weblab viwer from www.msi.com It supports a lot of formats and in
addition has the add H feature. As an alternative and for a short period
(20 days) you may wish to download the trial version of hyperchem
>from www.hyper.com . Both are for windows.

Hope this is of help..

Nikos Kourkoumelis
University of Ioannina
Greece

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> Does there exist any simple free available (Unix or windows) software
which
> is able to add
> hydrogens and/or atomic charges to PDB files?
>
>
> Thanks in advance,
> Eldbjørg S. Heimstad

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From: "김 한조" <[email-masked]>
Date: Fri, 10 Mar 2000 10:44:59 +0900

Dear CCLers and Heimstad,

I posted the same question on CCL and got some replies(thank the repliers ;->), but did not summarize them(and sorry for this :-<).
Though late, I hope this summary can be helpful.

1) VMD (http://www.ks.uiuc.edu/Research/vmd/)
 suggested by Ohyun Kwon(Auburn Univ.)
2) Gromacs (http://rugmd0.chem.rug.nl/~gmx) pdb2gmx in this package
 suggested by Marcel Swart
3) Weblab Viewer (http://www.msi.com)
 does not take pH as a parameter
4) Mol2Mol (http://www.compuchem.com)
 not in pH-dependent mode
 suggested by Dr Tamas E. Gunda(L. Kossuth University, Hungary)
5) Molden (URL: http://www.cmbi.kun.nl/~schaft/molden/molden.html)
 doesn't handle the effect of different pH's

Because the PDB file usually contains lots of atoms, 'add hydrogen' to it is not an easy task, and might need some manual editting(assign of file type, connectivity, etc.) if you want to convert it to other format(mol2, for example). Sometimes, Babel 1.6 seems not to work properly in my case.

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**************Kim Hanjo; Yonsei Univ., Dept. of Chemistry*************
****************82-2-361-2633(tel); 82-2-364-7050(fax)****************
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