Thanks for the answer Dr Case,
I just now realized a subtlety regarding gaff and gaff2 in my preparations.
In tleap, I sourced leaprc.gaff2, but in parmchk2 for generating the frcmod file, I never specified the -s 2 option for gaff2. It ran by default which is gaff. My input mol2 atom types are also gaff, not gaff2 as saved by Chinera. Never knew of the -s 2 option until you brought up differences between gaff and gaff2.
I wonder whether the whole time I was using gaff or gaff2, with the above mentioned procedure? Was sourcing leaprc.gaff2 compatible with gaff atom types, since it never reported an error?
Thank you.
> On Oct 15, 2020, at 1:32 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Thu, Oct 15, 2020, Liao wrote:
>
>> Thanks there, I could try preparing that, though for using vlimit=10,
>> does this seem like an appropriate solution? What’s the unit of this
>> parameter, the manual doesn’t say it. The trajectory as viewed and post
>> MD-MMGbsa energy from it looks normal to me.
>
> Units of vlimit are internal velocity usits: Å/(20 fs). vlimit=10 is
> OK, especially if it only get's triggered occasionally. But it does
> look like something in your ligand allows large forces: do you have any
> hydrogens with zero vdW radii? (This could happen on a ligand if you
> were, for example, using gaff rather than gaff2.) Hydrogens are a
> common source of headaches for non-standard residues.
>
> ....dac
>
>
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Received on Fri Oct 16 2020 - 15:00:02 PDT
