[gmx-users] gmx chi output clarification

[Francesco Carbone]

Thank you Justin,

I selected the atoms (CA-C-N-CA)  for the dihedral I want and check with
"gmx angle" (gmx angle -f  -n ciao.ndx -type dihedral)

If I use the trajectory (-f file.xtc and ndx from a gro file) I have a nice
distribution around 0° (avrg -3°) , while if I use the original pdb (-f
2bhl.pdb and ndx from pdb )  I have an average of -1°.
These results seem plausible, but why is "gmx chi" giving completely
different results when it checks the value in  a single structure?

Regards,

Francesco


On 16 February 2016 at 16:10, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/16/16 10:16 AM, Francesco Carbone wrote:
>
>> good afternoon,
>>
>> I'm trying to study the values of the omega dihedral (peptide bond) for a
>> specific Proline in my protein.
>> This Proline is known to exists in both cis and trans conformation(cis
>> while binding).
>>
>> In the pdb I used as starting point for the simulation (2bhl.pdb) the
>> Proline (172) is in cis configuration.
>> This is confirmed both by the people who make the pdb and also by vmd
>> ("fix
>> cis peptide bond" tool) .
>>
>> If I run the command:
>> gmx chi -s simulation.tpr -f simulation.xtc -o output.xvg -g logfile.log
>> -omega -all
>>
>> I can see that the Proline has values in the neighbourhood of 0° ( +-20°
>> ),
>> which is fine, being in cis.
>>
>> The problem is that if I try to calculate the same dihedral in the
>> original
>> structure (2bhl.pdb), using:
>> gmx chi -s 2bhl_fixed.pdb -f 2bhl_fixed.pdb -o output.xvg -g logfile.log
>> -omega -all
>> or
>> gmx chi -s 2bhl_fixed.pdb -f file.xtc -o output.xvg -g logfile.log -omega
>> -all
>>
>> I obtain values close to 180°,suggesting that  the Proline is in trans.
>>
>> How is it possible?
>>
>
> IIRC gmx chi does not use H atoms in the calculations of these dihedrals.
> Confirm with gmx angle -type dihedral that everything checks out.
>
> -Justin
>
>
>> I also tried to set -ramomega, but I don't see any xpm file being created.
>>
>> Am I doing something wrong?
>>
>> Regards,
>>
>> Francesco
>>
>>
> --
> ==================================================
>
> 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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