AMBER Archive (2006)

Subject: Re: AMBER: ptraj dumpq feature/bug

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Thu Aug 24 2006 - 15:16:23 CDT

Feature/Bug: you decide.

> I convert from mdrest format to pdb format with
> 'ambpdb -pqr -p hboth.prmtop < mdrest7 > mdrest7.pdb'
> in the output pdb file 'mdrest7.pdb' one has:
> /....
> ATOM 15277 O WAT 1006 16.453 -9.102 8.566 -0.8196 1.500
> ATOM 15278 H1 WAT 1006 17.625 -10.256 8.202 0.4564 1.200
> ATOM 15279 H2 WAT 1006 16.849 -8.812 9.406 0.3781 1.200
> ...
> ATOM 15826 O WAT 1189 8.566 16.453 -9.102 -0.8196 1.500
> ATOM 15827 H1 WAT 1189 8.202 17.625 -10.256 0.4564 1.200
> ATOM 15828 H2 WAT 1189 9.406 16.849 -8.812 0.3781 1.200
> ...
> ATOM 16375 O WAT 1372 -9.102 8.566 16.453 -0.8196 1.500
> ATOM 16376 H1 WAT 1372 -10.256 8.202 17.625 0.4564 1.200
> ATOM 16377 H2 WAT 1372 -8.812 9.406 16.849 0.3781 1.200
> ...../
>
> That is, some waters with special charges. This is ok.

Interesting that you have waters with different charges, but presumbly
this is by design.

> Now I try to strip all other waters except the ones listed above by:
...
> Now (in the file 'mdrest7_noH2O.pdb.1' the three waters listed above are there
> with the correct xyz positions,
> BUT WITH THE WRONG CHARGES for the last 2 waters:

Yes, this is bug/feature. The "strip" does not alter the charge array and
this is an oversight on my part as I never considered the dumpq option
with strip. You did nothing wrong and code change is necessary to fix
this.

--tom

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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