Hi,
Thanks for the two responses.
About solvent I only used igb=1 when performing simulated annealing
under NMR restraints (sa.in)
The prep directory is attached.
Many thanks for your help
sincerely
arnaud
Le 28/04/2020 à 23:02, Junmei Wang a écrit :
> Gaff adopted the good parameters from amber biomolecular force field. So
> the peptide-like parameters should be similar. For you minimization, did
> you consider solvent effect? If you send me your prep file, I will check if
> it is a force field issue or not.
>
> Best
>
> Junmei
>
> On Fri, Apr 24, 2020 at 11:02 AM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Fri, Apr 24, 2020, Arnaud Bondon wrote:
>>
>>> ). Clearly the N10 amide nitrogen
>>> has an pyramidal character. And the omega dihedral angles are not good
>>>
>>> The molecule was prepared as a mol2 file Nitrogen are N.am
>> The input atoms types don't matter: you should look at the output types
>> in the prep file. If this is a peptide-like molecule, it may be that
>> the gaff types don't do as well as the tuned Amber atom types.
>> You might want to see what happens if you request Amber atom types.
>>
>> I'm not sure whether GAFF has types that are specifically tuned for
>> peptide bonds or not...cc-ing Junmei here.
>>
>> ...good luck...dac
>>
>>
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--
POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
OU UN ETAT COMMUN
Arnaud BONDON
Equipe CORINT, UMR CNRS 6226
PRISM
CS 34317
Campus de villejean
Université de Rennes 1
35043 RENNES Cedex France
tel: (0)2 23 23 65 61
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Received on Wed Apr 29 2020 - 02:00:02 PDT
