[gmx-users] Tyrosine vsite aromatics

[David van der Spoel]

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se