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

[Dawid das]

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.

Best wishes,
Dawid


2014-08-06 18:49 GMT+01:00 Dawid das <addiw7 at googlemail.com>:

> Thank you Justin. It helped but in my *top file I have still the old
> connection and the new ones. Can I simply delete connection I do not want?
>
>
> 2014-08-06 2:32 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
>>
>> On 8/5/14, 11:59 AM, Dawid das wrote:
>>
>>> Dear Gromacs experts,
>>>
>>> I have found out why my force field does not work properly. I have added
>>> a
>>> new residue according to manual I found on Gromacs website. I modified
>>> all
>>> of the files. Now I have revealed that my new residue does not have
>>> connection to natural aminoacids in my topology file! If you take a look
>>> at
>>> it you will see that atoms 970 and 1009 are connected while the truth is
>>> that atoms 970 (carbonyl C atom of Phe65) and 1008 (MN1 atom of CH6 (new)
>>> residue) but also atoms 994 (MC3 atom of new residue) and 1009 (peptide N
>>> atom of Ser69) should be bonded. I have specified bonded parameters
>>> between
>>> those atom types in ffbonded.itp file but not in aminoacids.rtp.
>>> In other words my topology file does not recognize the connection between
>>> new residue and natural aminoacids residues. It seems like I do not
>>> specify
>>> something correctly in force field but I cannot find my mistake. Shall I
>>> specify this connection in specbond.dat file?
>>>
>>>
>> You do not need specbond.dat.  If the CH6 residue is an integral part of
>> the protein backbone, you need to specify the inter-residue bonds using the
>> +/- mechanism with appropriate atom names.
>>
>>
>> -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
>>
>> ==================================================
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>
>