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?
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Received on Mon Sep 17 2012 - 23:30:03 PDT
