Dear Amber users,
I have a query regarding the ATOMIC NUMBER section of the prmtop file in
case of a protein-ligand complex.
I referred to the 'Sustiva' example which is provided in the Amber
tutorials (
http://ambermd.org/tutorials/basic/tutorial4b/). As you can see,
in the Sustiva ligand, there is a CL atom. Following is the snippet from
the ligand prmtop file (sustiva.prmtop):
%FLAG
ATOM_NAME
%FORMAT(20a4)
*CL* F1 F2 F3 O1 O2 N C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11
C12 C13
C14 H122H121H112H111H101HN H5 H3 H2
-
-
%FLAG
MASS
%FORMAT(5E16.8)
*3.54500000E+01* 1.90000000E+01 1.90000000E+01 1.90000000E+01
1.60000000E+01
1.60000000E+01 1.40100000E+01 1.20100000E+01 1.20100000E+01
1.20100000E+01
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01
1.20100000E+01
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01
1.20100000E+01
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00
The MASS of CL is 35.45, which seems correct. The ATOMIC NUMBER section is
not present here, presumably because this prmtop file was generated with an
older version of AmberTools. As per appendix of Jason Swails' doctoral
dissertation (ambermd.org/prmtop.pdf), the ATOMIC NUMBER section was
included from AmberTools12. Hence I performed exactly the same exercise
with AmberTools12. Following is the snippet from this new ligand prmtop
file:
%FLAG
ATOM_NAME
%FORMAT(20a4)
*CL* F1 F2 F3 O1 O2 N C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11
C12 C13
C14 H122H121H112H111H101HN H5 H3 H2
-
-
%FLAG
ATOMIC_NUMBER
%FORMAT(10I8)
*6* 9 9 9 8 8 7 6
6 6
6 6 6 6 6 6 6 6
6 6
6 1 1 1 1 1 1 1
1 1
%FLAG
MASS
%FORMAT(5E16.8)
*3.54500000E+01* 1.90000000E+01 1.90000000E+01 1.90000000E+01
1.60000000E+01
1.60000000E+01 1.40100000E+01 1.20100000E+01 1.20100000E+01
1.20100000E+01
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01
1.20100000E+01
1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01
1.20100000E+01
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00
As you can notice, the value in the ATOMIC NUMBER section corresponding to
CL is 6 (which is atomic number of Carbon), but the MASS is 35.45, which is
atomic mass of Chlorine. The complex prmtop file is not provided in the
tutorial, so I prepared the complex in tleap with the same results for
Sustiva CL. (exactly the same parameters were used as in the tutorial).
Does anyone know why this is happening? Also, does Amber (sander/pmemd in
particular) use the ATOMIC NUMBER information during the simulation?
I would greatly appreciate your response.
Best Regards
Rohit
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Received on Fri Jan 31 2014 - 10:30:02 PST
