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

[Dawid das]

http://www.speedyshare.com/9EhEf/charm27-files.tar.bz2
http://www.speedyshare.com/AMWM7/mCherry7.tar.bz2

Like I said they are the same except two extra lines in aminoacids.rtp file.


2014-08-07 2:27 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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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