[gmx-users] gendr

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 16 12:45:18 CET 2001

On Fri, 16 Nov 2001, Luca Monticelli wrote:

>Dear all,
>I am trying to use the gendr program (present only in version 2.0), but I
>can't figure out what is the second input file -
>the manual only explains the first one. It looks like it has to contain
>"expansion mapping entries", but I am not sure what this means, and what's
>the correct format. Does anybody know?
This is looooooooooooooooong ago...

Anyway, if I recall correctly programs like xplor/cns sometimes write the
NMR input files, for e.g. a methyl group where you cannot distinguish the
protons, like
Ala MB
which then means all the protons on the CB
for gromacs this has to be expanded to
Ala HB1
Ala HB2
Ala HB3

There is also Q if you have two methyl groups, e.g. valine
Val QG would expand to
Val HG11
Val HG12
Val HG13
Val HG21
Val HG22
Val HG23

etc. I don't know what happened to the program, but maybe we threw it out
because it didn't work too well.

The mapping would thus have to describe the transofrmation in some way.

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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