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

[Justin Lemkul]

On 8/6/14, 12:52 PM, Dawid das wrote:
> Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to
> work it out then?
>

You'll need to provide files and describe exactly what the problems are (lines 
in the topology, please) and what changes you have made since the last bundle of 
files you uploaded.

-Justin

>
> 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.
>>

-- 
==================================================

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

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