Dear Jesper,
Creating your own atom type in this case is certainly reasonable and
Francois has outlined a good route for you. I would just add that in your
case, since you feel that the bond order is unusual, you may want to
specify your own force constant for this C-O bond (and perhaps also the
improper dihedral that controls the out of plane motion of the O) rather
than using it by analogy from others. Don't worry about getting this
exactly 'right' as the vibration of this O is unlikely to be a critical
motion in your system. It can be helpful to compare the vibrational
frequency of your C-O stretch (from nmode once you have built your new lib
file) to a QM calculation of the frequency (after appropriate scaling).
Cheers,
Brent
On Tue, Sep 18, 2012 at 2:26 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Jesper,
>
> I would just create a new atom type for this 'O'.
>
> See for instance: http://q4md-forcefieldtools.org/REDDB/projects/F-88/
> & http://q4md-forcefieldtools.org/REDDB/projects/F-88/script1.ff
> http://q4md-forcefieldtools.org/REDDB/projects/F-88/script3.ff
>
> this R.E.DD.B. project is a little complex and a little different from
> your needs; but it can help you. You can find there phenolate (or
> phenate) groups (which are connected to a metal; different to your
> case). The atom type used was OX.
>
> You define accurate equilibrium values (got from QM or exp. X-ray);
> get force constants by analogy to existing ones; the vdW param are
> taken from values available from parm99 (if you cannot find better).
>
> regards, Francois
>
>
>
> > To follow up on my problem a bit and perhaps add a bug, I have
> > looked at Tyrosine as an example and something puzzles me a bit.
> > In the "parm/parm10.dat" (I am using Amber11 just FYI). There are
> > sections with parameters for Tyrosine as shown here below. Some are
> > said not be in use anymore and some are said to replace these old
> > parameters.
> > What puzzles me is that it seems that the CZ (atomname) has been
> > changed in atomtype from C to CA.
> > However, when I look in "lib/amino10.lib" and "prep/amino10.in" the
> > atomtype is still C and not CA.
> >
> > Is this a bug/error or is this changed somewhere else?
> > Is this the same for ff12 in Amber12?
> >
> > Best regards,
> > Jesper
> >
> > C -CA 469.0 1.409 JCC,7,(1986),230; (not used any more in TYR)
> > C -OH 450.0 1.364 JCC,7,(1986),230; (not used any more for TYR)
> > CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
> > CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR
> > CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes;
> PHE,TRP,TYR
> > HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR
> > CA-OH 450.0 1.364 substituted for C-OH in tyr
> >
> > CA-C -OH 70.0 120.00 AA (not used in tyr)
> > CA-C -OS 70.0 120.00 phosphotyrosine
> > C -CA-HA 50.0 120.00 AA (not used in tyr)
> > CA-CA-OH 70.0 120.00 replacement in tyr
> > CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes
> > CT-CT-CA 63.0 114.00 AA phe tyr (SCH JPC 79,2379)
> > CX-CT-CA 63.0 114.00 AA phe tyr (SCH JPC
> > 79,2379) (was CT-CT-CA)
> > C -OH-HO 50.0 113.00 (not used in tyr anymore)
> > CA-OH-HO 50.0 113.00 replacement in tyr
> >
> > CA-CA-C -OH 1.1 180. 2. (not
> > used in tyr!)
> > CA-CA-CA-OH 1.1 180. 2. in tyr
> >
> >
> >
> >
> > On Sep 14, 2012, at 4:37 PM, Jesper Sørensen <jesorensen.ucsd.edu>
> wrote:
> >
> >> Hi all,
> >>
> >> I am trying to parameterize a ligand that contains a deprotonated
> >> phenol group.
> >> The oxygen is not exactly double bonded, but the C-O bond distance
> >> is very short (1.24 based on QM optimizations). Using parmcal this
> >> distance places it between a double bond (1.23) and a conjugated
> >> bond (1.26).
> >>
> >> I have been looking through the force field files for amber and
> >> gaff for a good atomtype for the oxygen, but I am not sure which
> >> one to use.
> >> Does anyone have a good suggestion for one to use, or should I
> >> proceed to create one on my own?
> >> In either case, would you suggest adding special bonded parameters
> >> for this bond, perhaps using values from parmcal?
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Associate Professor................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 18 2012 - 04:30:04 PDT
