AMBER Archive (2006)

Subject: AMBER: AMBER force field with namd

From: Fabien Cailliez (fabien.cailliez_at_ibpc.fr)
Date: Wed Feb 22 2006 - 11:54:23 CST

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,
Fabien

*******************************************
NAMD output :

Info: SUMMARY OF PARAMETERS:
Info: 1342 BONDS
Info: 76 ANGLES
Info: 35 DIHEDRAL
Info: 0 IMPROPER
Info: 0 VDW
Info: 153 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 13890 ATOMS
Info: 11410 BONDS
Info: 8777 ANGLES
Info: 9427 DIHEDRALS
Info: 0 IMPROPERS
Info: 26289 EXCLUSIONS
Info: 41667 DEGREES OF FREEDOM
Info: 5206 HYDROGEN GROUPS
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
%FLAG TITLE
%FORMAT(20a4)

%FLAG POINTERS
%FORMAT(10I8)
  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 Biochimie Théorique e-mail : cailliez_at_ibpc.fr IBPC 13, rue Pierre et Marie Curie 75005 Paris __________________________________________________________________

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