Jesper,
using AmberTools from Amber11: xleap -f leaprc.ff10
edit TYR
atom name CZ has the C atom type as in parm94.dat
in parm10.dat
C -CA 469.0 1.409 JCC,7,(1986),230; (not used any more in TYR)
-> but it looks like CZ has still the C atom type in amino10.lib
there is something wrong here: was it corrected in the last version of
the AmberTools?
In your case, I think it does not matter; I would still use a new type
for this phenolate oxygene atom.
regards, Francois
> 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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Received on Wed Sep 19 2012 - 13:00:02 PDT
