[gmx-users] gmx chi output clarification

[Francesco Carbone]

Thank you again for the quick response,

I read that, but I'm calculating the omega angle which shouldn't be
affected that how phi and psi are calculated.

Furthermore, if I'm wrong, -1° it's not simply "usually small" different
than 173°.

Regards,

Francesco


On 16 February 2016 at 17:30, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/16/16 12:26 PM, Francesco Carbone wrote:
>
>> 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?
>>
>>
> From the help info:
>
> * phi and psi dihedrals are calculated in a non-standard way, using
> H-N-CA-C
>   for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of
> N-CA-C-N(+).
>   This causes (usually small) discrepancies with the output of other tools
>   like gmx rama.
>
> So gmx chi is just using a different convention, one that you should be
> able to convert as needed.
>
> -Justin
>
>
> 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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>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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