[gmx-users] New residue in FF does not bond to others.

[Dawid das]

Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to
work it out then?


2014-08-06 19:45 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 8/6/14, 12:04 PM, Dawid das wrote:
>
>> Cause now what happens is that grompp requires bonding parameters for
>> atoms
>> which are actually bonded and for which are not (angle and dihedral
>> parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not want
>> connection between Ser69-Phe65. Now grompp asks me about bonding paramters
>> for atoms which build all three residues while these residues are
>> separated
>> by more than 4 atoms.
>>
>>
> Properly constructed .rtp entries will not need manual editing, which is
> very error-prone.  You're using lots of strange atom names, so you need to
> establish proper bonding from the CH6 residue; the +/- mechanism in
> flanking residues will fail.  If you're getting connections between
> non-consecutive residues, that suggests a break in the chain when being
> processed by pdb2gmx; make sure CH6 is defined as a Protein residue in
> residuetypes.dat.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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.
>