[gmx-users] regarding ligands in proteins

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 24 19:58:13 CEST 2001

On Wed, 24 Oct 2001, Luke Czapla wrote:

>  I would like to use that ffG43a1 force field (the Proteins only ffgmx
>force field won't work with Calcium ions), so I would need suitable
>replacements for CS1, OS, and HO (I don't know why using HO gives an
Maybe you can check the GROMOS96 paper for advice. The ffgmx force field
is basically the GROMOS87 in which these atomtypes were present. Maybe it
has turned out that these atom types are not necessary anymore. Indeed if
you look in the ffG43a1.rtp file you find entries for GLCA and GLCB which
look a lot like sugars, they do however use the normal CH1 etc. atomtypes.
You can thus modify the Glucose topology as indicated in the rtp file.
Or... If you rename your residue to GLCA, pdb2gmx should do it for you!

>  I followed your advice about pasting the coordinates into the .GRO file.
>However, when I go to run a position restraint or skip this to start the
>MD simulation (this is after energy minimization which I believe had a
>problem because the forces looked suspiciously high), I get this:
>Fatal error: Bond deviates more than half its own length
This could be because you pasted them in the wrong place.

But try renaming glucose first (be sure to take the right one!) and rerun

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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