[gmx-users] parameter for repeating units with cgenff

[Justin Lemkul]

On 12/12/15 1:59 PM, gromacs query wrote:
> Due to reasons, would it be possible for you to suggest off-list? I will
> really appreciate.
>

Sure, send me coordinates and your current topology.

-Justin

> 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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-- 
==================================================

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

==================================================