[gmx-users] gmx chi output clarification
Francesco Carbone
fra.carbone8 at gmail.com
Wed Feb 17 13:12:18 CET 2016
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?
Regards,
Francesco
On 16 February 2016 at 17:53, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>> --
>>> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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