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

[Dawid das]

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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