Lachele Foley писал 25.11.2017 08:37:
> "For preparing frcmod file, I first used the conversion of Gaussian
> output
> into the mol2 file then by the help of parmchk command made frcmod
> file."'
>
> What did you do with this frcmod file? You mention it but don't say
> how
> you use it.
>
> It really helps if you give full details. For example, Dave had to
> guess
> that maybe using shake will help. It would help if you show us the
> mdin
> files you are using.
>
> And, again, in your example, you built something called GLC and saved
> something called GLA. So, again, this cannot be what you actually did.
> It
> is very important to tell us exactly what you are doing. Please copy
> and
> paste the exact commands you used.
>
> BTW, there are no hydrogens with zero vdW parms in GLYCAM06j.dat
> (except
> the HW for TIP3P, which isn't really glycam). We got rid of such
> terms
> because we had observed behavior like what you describe, but not in
> plain
> glucose. With our charge sets, it would happen very, very rarely and
> only
> in very highly charged situations, for example when a carboxylate group
> was
> involved.
>
> If you are using charges you made yourself, it is possible that the
> charges
> are out of balance for the force field and that they are causing this
> behavior.
>
>
> On Fri, Nov 24, 2017 at 5:11 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Fri, Nov 24, 2017, Aashish Bhatt wrote:
>> >
>> > In the 0GA+ROH library,OH-O is not binding in the preparation of topology
>> > and coordinate file. but is getting bound in equilibration.
>>
>> This looks a lot like the case one can have when there is no
>> Lennard-Jones
>> (vdW) term on a H atom, and it can move arbitrarily close to a nearby
>> oxygen
>> atom. You should check the electrostatic energy at the point around
>> where
>> the
>> OH-O distance goes almost to zero: does it become very negative?
>>
>> If you have not done so, try turning on SHAKE for hydrogens (ntc=2).
>> If
>> the
>> dagnosis in the above paragraph is correct, that should prevent this
>> from
>> happening.
>>
>> [I'd like to encourage all Amber users to switch to gaff2, where there
>> are
>> no
>> longer any hydrogens with zero vdW parameters.]
>>
>> ...hope this helps....dac
>>
>>
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>>
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Received on Fri Nov 24 2017 - 23:30:02 PST
