[gmx-users] regarding ligands in proteins

[David van der Spoel]

On Wed, 24 Oct 2001, Luke Czapla wrote:

>
>Hi David,
>
>  I pdb2gmx-ed the glucose molecule replacing it as GLCA.  This worked
>very well, the only odd thing I noticed was that the total charge of the
>system went from -4.0 (which is what it is supposed to be) to -5.1.  I
>can't explain this.  I used the ffgmx force field.
If you look at the .top file you will see in the rightmost column the
cumulative charge. Whenever a residue has a non-integer charge you can
detect it here. Maybe your glucose is missing some hydrogens, or pdb2gmx
has made it part of the protein...

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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