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

[Justin Lemkul]

On 8/6/14, 1:36 PM, Dawid das wrote:
> These are lines that cause trouble:
>
> ERROR 1 [file mCherry7.top, line 18183]:
>    No default U-B types
>
>
> ERROR 2 [file mCherry7.top, line 18250]:
>    No default U-B types
>
>
> ERROR 3 [file mCherry7.top, line 25379]:
>    No default Proper Dih. types
>
>
> ERROR 4 [file mCherry7.top, line 25380]:
>    No default Proper Dih. types
>
>
> ERROR 5 [file mCherry7.top, line 25383]:
>    No default Proper Dih. types
>
>
> ERROR 6 [file mCherry7.top, line 25386]:
>    No default Proper Dih. types
>
>
> ERROR 7 [file mCherry7.top, line 25387]:
>    No default Proper Dih. types
>
>
> ERROR 8 [file mCherry7.top, line 25388]:
>    No default Proper Dih. types
>
>
> ERROR 9 [file mCherry7.top, line 25455]:
>    No default Proper Dih. types
>
>
> ERROR 10 [file mCherry7.top, line 25457]:
>    No default Proper Dih. types
>
> ERROR 11 [file mCherry7.top, line 25458]:
>    No default Proper Dih. types
>
>   Now in these files which I have already uploaded I have only added two
> extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp
> (lines 1793 and 1794):
>          MC3     +N      0.1345  154808.0
>          MN1     -C      0.139   173594.2
>
> I have not changed anything else in any other file.
> Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1
> atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6 is
> supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not supposed
> to be bonded to NH1 atom of Ser69 but it is in my *top file. What other
> files do you need?
>

The same ones you provided before.

-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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