[gmx-users] more questions

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 8 23:30:49 CEST 2001

On Mon, 8 Oct 2001, Luke Czapla wrote:

>  I have some more questions, that are unrelated to the glucose-binding
>protein.  I want to define a new type of residue that is formed by the
>sequence Ser-Tyr-Gly, post-translationally modified through an
>auto-cyclization reaction between Ser and Gly.  This is the chromophore
>found in many green fluorescent proteins.  I understand that defining
>new residues is best done by adding to the rtp (Residue topology file)
>with proper charges that match similar structures found in the force
>fields in gromacs.  
There may be a simpler way. If you just have a single bond between the two
residues you can add it to the specbond database. pdb2gmx will then look
for Ser-Gly combinations in bonding distance. So what is the chemical
nature of the link?

>  I would like to ask about what important things must be modified for
>simulations to work.  We are very much interested in hydrogen bonding, so
>anything regarding changes to the hydrogen database is important, and I
>have no idea if I need to edit the termini database or not to define this
>new residue.  Any advice on this would be appreciated, and an example of
>someone doing something like this (defining new residues) would be of
>incredible help!  Thanks
In general the format of the rtp files is quite straightforward, hdb is a
bit more difficult.

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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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