David Chan wrote:
Hi everyone
I am having some difficulty using 'vsite aromatics' for tyrosine
residues. I've made a pdb of a sole tyrosine residue and run it through:
pdb2gmx -f tyr.pdb -o tyr.gro -vsite aromatics -heavyh
using gromacs 3.3 and ffG43a2
Subsequently I put it into a box (editconf) and try to run an EM at
which point it explodes. ("This usually indicates your system is
exploding." msg in EM) When I run the same procedure with -vsite
hydrogens, the problem disappears.
I'm a bit confused because the gromacs 3.3 manual (e.g. Figure 6.4)
shows which dummy atoms should be generated and indicates that HH should
NOT be a virtual site. However, when I look in my topol.top file, the HH
atom is treated as a virtual site with no mass. In addition, the program
creates a virtual atom (MW1) in line with the OH-HH vector, 2 A from the
HH atom. As far as I can tell from the manual that virtual site should
not be there (?).
Vsite aromatics should be treated with care. This has to do with the
fact that the original implementation was for gromos87 and a lot was
hardcoded. The port to other force field was never completely stable in
our own hands anyway. Note the vsite hydrogens work correctly in
gromos96 and opls.
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 MNH3 1 TYR MN1 1 0 8.51535 ;
qtot 0
2 MNH3 1 TYR MN2 1 0 8.51535 ;
qtot 0
3 NL 1 TYR N 1 0.129 0 ;
qtot 0.129
4 H 1 TYR H1 1 0.248 0 ;
qtot 0.377
5 H 1 TYR H2 1 0.248 0 ;
qtot 0.625
6 H 1 TYR H3 1 0.248 0 ;
qtot 0.873
7 CH1 1 TYR CA 1 0.127 13.019 ;
qtot 1
8 CH2 1 TYR CB 2 0 14.027 ;
qtot 1
9 C 1 TYR CG 2 0 25.366 ;
qtot 1
10 C 1 TYR CD1 3 -0.1 0 ;
qtot 0.9
11 HC 1 TYR HD1 3 0.1 0 ;
qtot 1
12 C 1 TYR CD2 4 -0.1 0 ;
qtot 0.9
13 HC 1 TYR HD2 4 0.1 0 ;
qtot 1
14 C 1 TYR CE1 5 -0.1 25.366 ;
qtot 0.9
15 HC 1 TYR HE1 5 0.1 0 ;
qtot 1
16 C 1 TYR CE2 6 -0.1 25.366 ;
qtot 0.9
17 HC 1 TYR HE2 6 0.1 0 ;
qtot 1
18 C 1 TYR CZ 7 0.15 0 ;
qtot 1.15
19 OA 1 TYR OH 7 -0.548 16.5034 ;
qtot 0.602
20 MW 1 TYR MW1 7 0 0.504 ;
qtot 0.602
21 H 1 TYR HH 8 0.398 0 ;
qtot 1
22 C 1 TYR C 9 0.27 12.011 ;
qtot 1.27
23 OM 1 TYR O1 9 -0.635 15.9994 ;
qtot 0.635
24 OM 1 TYR O2 9 -0.635 15.9994 ;
qtot 0
I searched the mailing list and was only able to find this thread that
seems to be related, but not quite the same:
http://www.gromacs.org/pipermail/gmx-developers/2002-June/000239.html
This seems odd to me as this should have created problems earlier, no?
Or am I missing something obvious?!
Thanks a lot for any suggestions!
David
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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