AMBER Archive (2009)

Subject: Re: [AMBER] ask for parm99MOD

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu May 28 2009 - 15:56:14 CDT

HI all,
I just re-read the Proteins paper you sent to all.
Indeed, the parmmod2 used there was the one used to fold trp-cage.
As carlos mentioned, this is an early version of ff99SB.

Use ff99SB and you should be fine.
Adrian

Carlos Simmerling wrote:
> I see- I think you need to check with Alexey Onufriev but that may have been
> an early version of ff99SB.
> read the ff99SB paper to see the differences between ff99 and ff99SB. do not
> use ff02 or anything related- you'll get confused, since that has little to
> do with ff99.
> if you want to comapre ff99 and ff99SB, use those files in leap. don't use
> ff02 unless that is really what you want.
>
> On Thu, May 28, 2009 at 4:32 PM, xiaoqin huang <xqhuang1018_at_msn.com> wrote:
>
>>
>>
>>
>>
>>
>>
>> I use ff02, but parm99.dat is loaded into xleap when source leaprc.ff02. I
>> want to see the difference between parm99.dat and parm99MOD2 for my protein
>> when using the same PBradii mbondi2. According to the reference of GB-OBC
>> model, the parm99MOD2 is better.
>>
>>
>>
>>> From: carlos.simmerling_at_gmail.com
>>> Date: Thu, 28 May 2009 16:22:31 -0400
>>> Subject: Re: [AMBER] ask for parm99MOD
>>> To: amber_at_ambermd.org
>>>
>>> no- do you mean ff99 or ff02? they are different force fields.
>>>
>>> On Thu, May 28, 2009 at 4:09 PM, xiaoqin huang <xqhuang1018_at_msn.com>
>> wrote:
>>>> thanks, I mean parm99.dat that was included in ff02. is this statement
>>>> proper?
>>>>
>>>>
>>>>
>>>>> From: carlos.simmerling_at_gmail.com
>>>>> Date: Thu, 28 May 2009 15:57:24 -0400
>>>>> Subject: Re: [AMBER] ask for parm99MOD
>>>>> To: amber_at_ambermd.org
>>>>>
>>>>> do you mean parm99 or ff02? these are different force fields. keep in
>>>> mind
>>>>> that ff02 has many differences including charge model, so direct
>>>> comparison
>>>>> is very difficult. comparison to ff99 is most direct but this is not
>> a
>>>> good
>>>>> force field. if you are talking about the protein force field that I
>>>> think
>>>>> you are, it is a modification of something my lab published a while
>> back.
>>>> it
>>>>> was an early version of ff99SB, but had serious problems with Gly
>>>> dihedrals,
>>>>> which
>>>>>
>>>>>
>>>>> On Thu, May 28, 2009 at 3:51 PM, xiaoqin huang <xqhuang1018_at_msn.com>
>>>> wrote:
>>>>>> yes, thanks, I want to test this parm99MOD2 on the protein I am
>>>> simulating,
>>>>>> and compare with that of parm99.dat used in ff02.
>>>>>>
>>>>>>> From: carlos.simmerling_at_gmail.com
>>>>>>> Date: Thu, 28 May 2009 15:44:41 -0400
>>>>>>> Subject: Re: [AMBER] ask for parm99MOD
>>>>>>> To: amber_at_ambermd.org
>>>>>>>
>>>>>>> my personal opinion is that modifying backbone dihedral
>> potentials to
>>>>>>> correct for problems in the solvent model is not going to be
>>>> transferable
>>>>>>> among systems. also be very careful if you use this force field
>> to
>>>>>> exactly
>>>>>>> math the GB model and radii to the ones used in the training.
>>>>>>>
>>>>>>>
>>>>>>> On Thu, May 28, 2009 at 3:41 PM, xiaoqin huang <
>> xqhuang1018_at_msn.com>
>>>>>> wrote:
>>>>>>>> sorry, I mean parm99MOD2, which is good for GB simulations.
>>>>>>>>
>>>>>>>>
>>>>>>>>> Date: Thu, 28 May 2009 15:38:23 -0400
>>>>>>>>> From: roitberg_at_qtp.ufl.edu
>>>>>>>>> To: amber_at_ambermd.org
>>>>>>>>> Subject: Re: [AMBER] ask for parm99MOD
>>>>>>>>>
>>>>>>>>> would you mind clarifyng what the parm99MOD is ?
>>>>>>>>> I have a suspicion that you refer to the hornak et al force
>>>> field,
>>>>>> which
>>>>>>>>> would then can be found in amber as 99SB
>>>>>>>>>
>>>>>>>>> Adrian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> xiaoqin huang wrote:
>>>>>>>>>> got it, modify 4 torsional potentials.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> From: xqhuang1018_at_msn.com
>>>>>>>>>>> To: amber_at_ambermd.org
>>>>>>>>>>> Date: Thu, 28 May 2009 14:16:35 -0400
>>>>>>>>>>> Subject: [AMBER] ask for parm99MOD
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> hi, anyone can help me to find where is the parm99MOD set?
>> I
>>>> need
>>>>>> it
>>>>>>>> for GB simulations.
>>>>>>>>>>> thanks a lot
>>>>>>>>>>>
>>>>>>>>>>> xiaoqin
>>>>>>>>>>>
>>>>>>>>>>> 05/28/2009
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>> _________________________________________________________________
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>>>>>>>>> --
>>>>>>>>> Dr. Adrian E. Roitberg
>>>>>>>>> Associate Professor
>>>>>>>>> Quantum Theory Project
>>>>>>>>> Department of Chemistry
>>>>>>>>>
>>>>>>>>> Senior Editor. Journal of Physical
>> Chemistry
>>>>>>>>> American Chemical Society
>>>>>>>>>
>>>>>>>>> University of Florida PHONE 352
>> 392-6972
>>>>>>>>> P.O. Box 118435 FAX 352
>> 392-8722
>>>>>>>>> Gainesville, FL 32611-8435 Email
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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