[gmx-users] regarding ligands in proteins

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 26 15:27:50 CEST 2001

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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