[gmx-developers] Re: [gmx-users] NMR Refinement

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 13 16:51:13 CET 2002

On Wed, 13 Mar 2002, Patrick Ladam wrote:

>Allright I found this at the end of the topoly file in nmr1 demo. 
>Thought the way it is handled is not really suitable for NMR refinement 
>process as it uses aton numbers which is not really directly human 
>readable (who is atom number 635 already???). In my case I have more
>than 500 dist restraints, this is comon in NMR. The NMR refinement 
process is based on going back and forth between NMR data interpretation
>and Modelling results to check for dist+diedral violations and 
>reconsider the NMR data interpretation in a cyclic manner.
>So working with constraint files holding atom numbers is not really 
>easy, not to say undoable
>when having a large number of constraints.
>It would be of a great help if one could have a dist constraint file formated
>something like:
>Resid 1 atom HA  Resid 35 atom HB 3.5   0.5   0.5
>for instance, same type of thing for diedral angles.
>I just want to highlight the fact that this type of format precludes NMR
>spectroscopist from working with GMX which is too bad because I think it 
>really is a nice piece of software (excellent doc, ease of use compared 
>to CNS...). Why not consider to incorporate CNS or DYANA restraint files 
>importation in next releases, I can help providing the file formats of 
>several NMR refinement programs.

Reading in a CNS file is not too difficult probably. Ideally that should 
be done in grompp or so, rather than having to edit the topology. Post 
some files on the list, no promises though...

Analysis of the output is another thing. There is an analysis program 
(g_disre) which finds the largest violations for you, and prints them to 
a log file (in readable format I think).

Furthermore GROMACS has some features for refinement that not many 
other packages have (I think...)

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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