AMBER Archive (2006)

Subject: Re: AMBER: AMBER force field with namd

From: Vlad Cojocaru (
Date: Thu Feb 23 2006 - 04:11:17 CST

Dear Fabien,

Maybe it would be best to post this on the NAMD list .... People could
help you more I believe ...

First of all, as far as I am aware new versions of NAMD do not require
any change of the amber topology for the waters ... Its bin quite a
while since I used NAMD and I remember that I had to change the water
box ... but as far as I understood the newest versions of NAMD do treat
the 3-bonded waters properly ... You should though check with namd
people to be sure ... Or run a short simultation with a topology having
3-bonded waters.. If you monitor the angle H-O-H during the simulation
and it shrinks ...than you should change the topology but if it stays
constant you dont have to change the topology...

As for the impropers, as far as I remember this was a harmless message
but I do not remember exactly why (I would have to dig into my notebooks
for that)... maybe its because NAMD treats the impropers as normal
dihedrals ... (please take this as a guess rather than a fact .... maybe
check the number of dihedrals ) ...

As for the exclusions, I cannot help you with that ... sorry ...


Fabien Cailliez wrote:

>Dear AMBER users,
>I am trying to use AMBER force field with NAMD.
>The first problem is about defining TIP3P waters with no H-H bond and with HOH angle.
>So I changed leap according to what is told in the AMBER list (and also the solvents.cmd to remove H-H bond)
>and the topology file thus created seems OK. However, when I load it with NAMD, I see two weird things :
>- the number of improper torsions read by NAMD is 0 whereas leap tells me that
>the number of improper torsions added is 553.
>- thenumber of exclusions read by NAMD (26289) does not match with the number of exclusion terms
>in my topology file (30243).
>I put both the output of NAMD and the beginning of my topology file at the end of the mail.
>Did someone ever noticed that or did I compare the wrong numbers ?
>When this problem is fixed, I would like to compare AMBER results with NAMD results from the same starting point
>to check that everything is OK. But there is another problem then :
>I cannot load the modified topology file into sander because it tells me :
>Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds.
>Residue 357 contains 2 bonds.
>Thanks in advance for your help and suggestions,
>NAMD output :
>Info: 1342 BONDS
>Info: 76 ANGLES
>Info: 35 DIHEDRAL
>Info: 0 VDW
>Info: 153 VDW_PAIRS
>Info: ****************************
>Info: 13890 ATOMS
>Info: 11410 BONDS
>Info: 8777 ANGLES
>Info: 9427 DIHEDRALS
>Info: 26289 EXCLUSIONS
>Info: TOTAL MASS = 104743 amu
>Info: TOTAL CHARGE = -7 e
>Info: *****************************
>Topology file :
>%VERSION VERSION_STAMP = V0001.000 DATE = mm/dd/yy hh:mm:ss
> 13890 17 8684 2726 6853 1924 5985 3442 0 0
> 30243 3997 2726 1924 3442 1342 76 35 28 1
> 0 0 0 0 0 0 0 0 24 1
> 0 0
>-- __________________________________________________________________ Fabien Cailliez Tel : 01 58 41 51 63 Laboratoire de Biocchimie Théorique e-mail : IBPC 13, rue Pierre et Marie Curie 75005 Paris __________________________________________________________________
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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