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 (?).
[ 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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