[gmx-users] parameter for repeating units with cgenff

[gromacs query]

Due to reasons, would it be possible for you to suggest off-list? I will
really appreciate.

Thanks.

On Sat, Dec 12, 2015 at 6:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/12/15 1:25 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Somehow I can not use available units in CHARMM library. The best thing I
>> could achieve as of now is using CGenFF. I created a side chain terminated
>> with some atoms (cap) which are same as in the next attaching unit
>> (directly available in CHARMM). After removing caps from the side chain
>> and
>> some atoms from second attaching unit I can generate a full combined unit
>> but with formal net charge being 0.002. This seems to be very less but can
>> I spread this charge (manually) on other atoms to get a nice 0.000 formal
>> charge as this residual charge will add up as I have many such units. I
>> have tried different combinations but this is the minimal formal charge I
>> was able to achieve.
>>
>>
> There should be a way to assign the charges intuitively if you have capped
> the units appropriately.  Without knowing the chemical structure you're
> working with, I can't (and won't) blindly suggest anything.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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