From: John Baker (pcxjb3_at_nottingham.ac.uk)
Date: Wed Dec 07 2011 - 05:38:11 CST
Hello,
I have been using NAMD for a while, but I have recently began using the
FEP module to measure free energy differences of molecules in solvents.
I am looking at the alchemical transformation of methanol --> ethane in
water.
The problem I am having is that the methanol carbon changes charge from
0.265 to 0, and therefore I need to include three carbon atoms.
I placed two carbon atoms in the pdb with the same coordinates, but with
different charges (C2, C3).
Below is the PDB and PSF for the transformation in a vacuum.
ATOM 1 C1 LIG 1 0.000 0.000 0.000 1.00 0.00 C
ATOM 2 C2 LIG 1 0.000 0.000 1.530 1.00 0.00 C
ATOM 3 H1 LIG 1 1.026 0.000 -0.373 1.00 0.00 H
ATOM 4 H2 LIG 1 -0.512 0.888 -0.373 1.00 0.00 H
ATOM 5 H3 LIG 1 -0.513 -0.888 -0.373 1.00 0.00 H
ATOM 6 H4 LIG 1 0.513 0.888 1.903 1.00 0.00 H
ATOM 7 H5 LIG 1 0.512 -0.888 1.903 1.00 0.00 H
ATOM 8 O1 LIG 1 -1.344 0.000 2.019 1.00 0.00 O
ATOM 9 H6 LIG 1 -1.677 0.019 2.919 1.00 0.00 H
ATOM 10 C3 LIG 1 0.000 0.000 1.530 1.00 0.00 H
ATOM 11 H7 LIG 1 -1.025 0.000 1.903 1.00 0.00 H
END
11 !NATOM
1 O1 1 LIG C1 CR 0.000000 12.0110 0
2 O1 1 LIG C2 CR 0.265000 12.0110 0
3 O1 1 LIG H1 HCMM 0.000000 1.0079 0
4 O1 1 LIG H2 HCMM 0.000000 1.0079 0
5 O1 1 LIG H3 HCMM 0.000000 1.0079 0
6 O1 1 LIG H4 HCMM 0.000000 1.0079 0
7 O1 1 LIG H5 HCMM 0.000000 1.0079 0
8 O1 1 LIG O1 OR -0.700000 15.9994 0
9 O1 1 LIG H6 HOR 0.435000 1.0079 0
10 O1 1 LIG C3 CR 0.000000 12.0110 0
11 O1 1 LIG H7 HCMM 0.000000 1.0079 0
12 !NBOND: bonds
1 2 2 6 2 7 2 8
3 1 4 1 5 1 8 9
10 1 10 6 10 7 10 11
When I run the simulation I receive an error of bad hydrogen group size
on atom 2, although atom 2 is the methanol carbon and is connected to
1C, H4, H5 and O1.
Please advise, I can't see anything wrong with the hydrogen counts.
Many thanks in advance,
John Baker (PhD candidate, University of Nottingham)
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