Jason Swails wrote:
Thank you Jason and Yildirim for your comments
> Hello,
>
> A couple of comments:
>
> 1. All gaff atom types are lower-case
>
Agree !! but this force parameter are constructs for simulations with
GROMACS where the AMBER is now supported.
> 2. Are you building an amber topology file? I'm not familiar with using an
> Amber package to set up a gromacs simulation.
>
No it is for GROMACS, Briefly i have constructed a pdb file for the TFE
molecule. I have added in my topology file the parameters for the TFE
with the assigned atome types taken from gaff. The charges for each TFE
atoms were taken from RED.DB server. Finally the bonded parameters taken
from gaff were converted into the GROMACS format.
> 3. If you are creating an amber topology file and converting it later, you
> should add missing parameters to an frcmod file rather than directly editing
> gaff.dat.
> 4. Not all parameters for all molecules will exist in gaff.dat.
Probably, but the trifluoroethanol is a (very) common molecule used in
biomolecular simulations. So it is strange for me that some parameters
for this molecule are missing in GAFF or others AMBER ff (AFAIK)
> You can use
> parmchk to see if any generic terms match the dihedral you're looking for
> (i.e. using X as wild-cards for the 1,4 groups).
> 5. If any are missing, you'll need to determine what those are (i.e. by
> comparing to quantum results) and put them in the frcmod file
>
Yes it is a possibility
Stephane
> Good luck!
> Jason
>
> On Fri, Jan 21, 2011 at 9:51 AM, Stephane Abel <Stephane.Abel.cea.fr> wrote:
>
>
>> Dear AMBER users,
>>
>>
>> I am trying to build the trifluoroethanol parameters from GAFF force
>> field for MD with GROMACS code. For this purpose the parameters in the
>> GAFF.dat file given in the ambertools package (v. 1.4). I have defined
>> the TFE atome types as follows :
>>
>>
>> [ TFE]
>> [ atoms ]
>> C1 C3 0.64900 1 <---- C3 is as a Sp3 C
>> (correct ?)
>> C2 C3 0.09760 2
>> O1 OH -0.57850 3
>> F11 F -0.23790 4
>> F12 F -0.23790 5
>> F13 F -0.23790 6
>> H21 HC 0.06200 7
>> H22 HC 0.06200 8
>> H3 HO 0.42150 9
>> [ bonds ]
>> C1 C2
>> C1 F11
>> C1 F12
>> C1 F13
>> C2 O1
>> C2 H21
>> C2 H22
>> O1 H3
>>
>>
>> I can define all the bond and angle parameters. But for dihedral
>> parameters, the OH C3 C3 F quadruplet is not present in the
>> gaff.dat file.
>>
>>
>> Any advice is welcome
>>
>>
>> Stephane
>>
>>
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
>
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Received on Fri Jan 21 2011 - 08:00:06 PST
