namd and amber force field

From: Fabien Cailliez (
Date: Thu Feb 23 2006 - 11:38:01 CST

Dear all,

I am trying to use namd with AMBER force field and I have few questions about
I read about problems of H-H bonds and HOH angles in TIP3P waters that are
present in AMBER topology files and are not good for namd. But I also read in
the namd wiki that it should be fixed in new versions > 2.5b3.
I would like to know if this is really the case in namd 2.6, because I do not
see major differences between output from namd2.5 and namd2.6b1 with a
warning about H-H bonds.

The other questions concern parameters read in the AMBER topology file.
I checked if there were well read byt comparing values from the output of namd
and of my topology file. There are two problems concerning exclusion terms
and improper torsions (I get a message in my output from namd saying that
exclusions are read from PARM file).
In my ouput file, I get 26289 exclusions and 0 improper, whereas I have in
fact 30243 exclusion terms in my AMBER files and 553 improper dihedrals.
Is there a reason explaining these two differences (the other parameters are
read correctly) ?

Thank you in advance for your help,

Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail :
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					

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