[gmx-users] parameter for repeating units with cgenff

gromacs query gromacsquery at gmail.com
Fri Dec 11 18:17:54 CET 2015

Hi Justin

Thanks for the reply. Yes your are right and indeed, sorry I forgot to
mention, I tried with some CH3 and other groups which may be considered as
an appropriate 'cap' which is normally followed by many. But in this case I
will have to remove the cap e.g. B-O-CH3 to B-O- before joining to the next
residue. This causes a net non-integral charge on B-O- which is not correct
as disturbs overall integral charge of the polymer. Ideally the cap once
removed should leave B-O with integral charge. I have tried many caps but
none of them after being removed leave B-O to be integral.

best regards,

On Fri, Dec 11, 2015 at 4:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 12/11/15 10:17 AM, gromacs query wrote:
>> Hi All,
>> I am using cgenff to derive parameters for some polymer (A-BBBB...-C). The
>> repeating block B has some Oxygen O atom which joins the next residue
>> (-BO-). When I derive charges for B residue with cgenff then I get net -1
>> charge on B residue because of this unsatsified O atom. I want to keep B
>> residue formal charge zero. I get formal charge zero if I derive charges
>> on
>> B-OH residue but removing H will again will give some non-intergral formal
>> charge. I am not sure what should done in this regard.
>> If someone has some experience with this or suggestion I will highly
>> appreciate it.
> To derive suitable monomer units, you have to include all the linking
> atoms; if it's an ether of some sort, you need B-O-CH3 or whatever is
> similar to then apply to the actual polymer itself.  Just parametrizing B
> in the absence of flanking atoms is inappropriate.
> -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
> ==================================================
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list