[gmx-users] Problem with g_chi options

Florian Sittel sittel at lettis.net
Sun Aug 3 16:39:52 CEST 2014


I've just encountered exactly the same problem.
I have a trajectory from another group and a .pdb-file with the 
reference structure.
 From the pdb I generated a tpr file, however g_chi finishes with these 

'57 residues with dihedrals found
276 dihedrals found
Reading frame  1514000 time 75667.297
j after resetting (nr. active dihedrals) = 170

WARNING: not all dihedrals found in topology (only 170 out of 276)!'

This suggests, that it can only find the backbone dihedrals, but not the 
of the sidechains.

I do not get, what is meant by 'active dihedrals'.

Additionally, if g_chi relies on topological information from a tpr-like 
we should perhaps change this help

'-s       conf.gro  Input        Structure file: gro g96 pdb tpr etc.'

(like in g_rama).

Any little hints to this problem are highly welcome.


On 07/14/2014 04:33 PM, Anna Stopka wrote:
> Hi!
> Thanks for your reply Justin!
> I have tried using a tpr file instead of a gro file, but that makes no 
> difference. I still have the same problem!
> Does anybody have another idea?
> Thanks in advance!
> Anna
> On 07/09/2014 07:24 PM, Justin Lemkul wrote:
>> On 7/9/14, 5:51 AM, Anna Stopka wrote:
>>> Hi everybody,
>>> I wrote last week, but nobody answered. So I write again, still 
>>> having the same
>>> problem:
>>> I want do an analysis of my simulation with the tool g_chi.
>>> The problem is, that the optional output options don't work.
>>> I use the following command:
>>> g_chi -s config.gro -f traj.xtc -oh -all
>>> and all I get are the standard output files chi.log and order.xvg.
>>> I am not sure if it has something to do with the following warning I 
>>> get:
>>> WARNING: not all dihedrals found in topology (only 1056 out of 1746)!
>>> Honestly, I don't understand why I get this warning, because all the
>>> input files are fine.
>> Have you tried using a .tpr file instead of a .gro file as the 
>> structure passed
>> to -s?  I don't know how there can be any interpretation of a 
>> topology, given
>> the fact that you haven't passed any topological information to g_chi.
>> -Justin

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