Dear Jesper,
> I looked and I think its the same for Ambertools12, so you agree
> this is a bug?
> It doesn't really relate to my problem exactly, but since my protein
> system does contain Tyrosine residues it does seem important.
I do not know if it is a bug. Some comments are just ambiguous; but
the FF works as it was originally defined...
regards, Francois
> On Sep 19, 2012, at 12:39 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> 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?
>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 19 2012 - 22:30:02 PDT
