[gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/23/17 11:06 PM, Sailesh Bataju wrote:
>>> * Making bonds...
> *>>* Warning: Short Bond (5-1 = 0.0259999 nm)
> *>>* Warning: Long Bond (5-6 = 0.99084 nm)
> *>>* Warning: Long Bond (1-2 = 0.944378 nm)
> *>>* Warning: Long Bond (1-3 = 0.895661 nm)
> *>>* Warning: Long Bond (1-4 = 0.866986 nm)
> *>>* Warning: Long Bond (7-8 = 0.502204 nm)
> *>>* Warning: Long Bond (7-9 = 0.567317 nm)
> *>> *Warning: Long Bond (7-10 = 0.92202 nm)
> *>>* Warning: Long Bond (11-12 = 0.592831 nm)
> *>>* Warning: Long Bond (11-13 = 0.700231 nm)
> *>>* Warning: Long Bond (11-14 = 0.729592 nm)*
>
>> The short bond warnings do, however, indicate that the starting geometry is bad.
>
>> -Justin
>
> I'd a doubt about it you eventually pointed it out sir, thank you.
> Those bond lengths have drastic differences than the bond lengths
> given in ffbonded.itp file. Here it goes according to the .itp file:-
>
> 1-5 = 0.15380000 nm
>
> 5-6 = 0.11110000 nm
>
> 1-2 = 0.11110000 nm
>
> and so on...
>
> Nothing has matched with those generated bonds. It looks like I've to
> modify pdb file manually for correct geometry using distance formula
> or is there some other way to do it, sir?
>

Extract the coordinates of any valine side chain in a protein, make an IBUT .hdb 
entry based off of it (all you'll need to do is change 2 -> 3 in the number of H 
added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms 
for you.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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