Hi Francois,
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.
Best,
Jesper
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?
>
>
>
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Received on Wed Sep 19 2012 - 13:00:03 PDT
