[gmx-users] gmx chi output clarification

[Justin Lemkul]

On 2/16/16 12:40 PM, Francesco Carbone wrote:
> 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.
>

http://skryb.info/m/gmx-users@gromacs.org/438C0B56.4020606@xray.bmc.uu.se

Looks like omega here is calculated as O-C-N-CA, not CA-C-N-CA.  Check the code 
to be sure.

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

It is if the convention is flipped and 173 actually indicates -7.

Clearly the gmx chi help info needs some more work.

-Justin

> 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
>>
>> ==================================================
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>> Gromacs Users mailing list
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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

==================================================