[gmx-users] OPLS modification between 3.3 and 3.3.1??

[Erik Lindahl]

Hi Chris,

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).

Cheers,

Erik

On Apr 19, 2006, at 9:41 PM, chris.neale at utoronto.ca wrote:

> Hello,
> 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
> ~/TEST/gromacs-3.3.1/share/top/ffoplsaa.rtp
> 1008,1010c1008,1010
> <     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
> 1025c1025
> <     CG    opls_210    0.0975    3
> ---
>>     CG    opls_210    0.048     3
> 1028,1029c1028,1029
> <     SD    opls_202   -0.435     4
> <     CE    opls_209    0.0375    5
> ---
>>     SD    opls_202   -0.335     4
>>     CE    opls_209   -0.013     5
> 1325,1326c1325,1326
> <      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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>