[gmx-users] OPLS modification between 3.3 and 3.3.1??
lindahl at sbc.su.se
Wed Apr 19 22:50:39 CEST 2006
This change was committed before we had started bugzilla, so thus no
entry, but you can find it in the CVS log :-) It was covered on the
mailing list, though.
The torsion only affects non-standard protonation states of side
chains that are not present in any OPLS-AA publication. The old
version used the "standard" values (i.e., not OPLS-AA/L) while the
newer ones just copy the OPLS-AA/L value. I really have no idea which
one is better - the proper solution is for somebody to reparametrize
it. In any case you will never get those residues unless you specify
the protonation state manually.
The charge distribution in MET has been modified to agree with later
OPLS-AA/L values (instead of the 2000 ones).
On Apr 19, 2006, at 9:41 PM, chris.neale at utoronto.ca wrote:
> ffoplsaa.rtp has changed in the 3.3.1 release. However, there are
> no references
> given and no special notification of this fact. I was wondering if
> anybody knows
> the references for this change.
> Here is the difference between the two distributions:
> diff ~/TEST/gromacs-3.3/share/top/ffoplsaa.rtp
> < CD CE NZ HZ1 dih_LYSH_chi5_C_C_N_H
> < CD CE NZ HZ2 dih_LYSH_chi5_C_C_N_H
> < CD CE NZ HZ3 dih_LYSH_chi5_C_C_N_H
>> CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
>> CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
>> CD CE NZ HZ3 dih_LYS_chi5_C_C_N_H
> < CG opls_210 0.0975 3
>> CG opls_210 0.048 3
> < SD opls_202 -0.435 4
> < CE opls_209 0.0375 5
>> SD opls_202 -0.335 4
>> CE opls_209 -0.013 5
> < N CA CB CG dih_GLU_chi1_N_C_C_C
> < CG CB CA C dih_GLU_chi1_C_C_C_CO
>> N CA CB CG dih_TRP_chi1_N_C_C_C
>> CG CB CA C dih_TRP_chi1_C_C_C_CO
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