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 Bioochimie Théorique e-mail : cailliez.ibpc.fr IBPC 13, rue Pierre et Marie Curie 75005 Paris __________________________________________________________________
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Received on Sun Feb 26 2006 - 06:10:14 PST
