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

Justin Lemkul jalemkul at vt.edu
Wed Aug 6 03:33:02 CEST 2014

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 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


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