[gmx-users] gmx chi output clarification

[Francesco Carbone]

thank you Justin,
kind as always!
I hope that David (or who knows gmx chi better) will have a look at this
post soon.

In the meanwhile I'll use gmx chi (5.0.4), having care of keeping an eye on
the results , and comparing them with other source.

Regards,

Francesco

On 17 February 2016 at 12:49, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/17/16 7:11 AM, Francesco Carbone wrote:
>
>> Thank you Justin,
>>
>> I'm not a pro in C, but I think that in the code, the omega angle is
>> defined as CA-C-N-CA (Bug #953 discussed this)
>> ...
>> dl[i].j0[edOmega] = n/4;
>> id[n++] = dl[i].atm.minCalpha;
>> id[n++] = dl[i].atm.minCalpha;
>> id[n++] = dl[i].atm.N;
>> id[n++] = dl[i].atm.Cn[1];
>> ...
>>
>> I then calculated the same angle using gmx chi (5.0.4) , g_chi (4.6), gmx
>> angle (5.0.4) and pdbtorsion (an in house tool that is always right ,of
>> course this is what my supervisor says :D)
>>
>> If I use pdbs dumped from a trajectory, all of them provides similar
>> values
>> (3-4-0.2-1).
>> On the other hand, if I'm using a pdb coming from outside source (
>> rcsb.org),
>> gmx chi is the only one that gives "flipped" values.
>> If I remove the flip (173 -180° ) I obtain a plausible value, but then why
>> don't I see this "flip" when I use "gmx chi" with a trajectory or a pdb
>> dumped from the trajectory?
>>
>>
> Hopefully whoever wrote the code (David?) will comment, as this is the
> extent of what I know about gmx chi (since I haven't used it in a long
> time).
>
> -Justin
>
>
> --
> ==================================================
>
> 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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