Thank you both Brent and Francois for that answer. I'll add an atomtype and see how that works.
I am still puzzled by the force field information regarding Tyrosine. Is that a bug?
Best,
Jesper
On Sep 18, 2012, at 4:22 AM, Brent Krueger <kruegerb.hope.edu> wrote:
> 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?
>>
>>
>>
>> _______________________________________________
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>> 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
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Received on Tue Sep 18 2012 - 16:00:03 PDT
