[gmx-users] Re: modeling a chromophore residue

Luke Czapla czapla at rutchem.rutgers.edu
Wed Oct 10 23:38:00 CEST 2001

Hi David,

  Thank you for this excellent method.  The question about how flat is
complicated.  It is completely flat in the crystal structure, but I'd
really have to think about the vibrational modes to give you a good answer
to that question.  I would say we can assume it's completely flat because
of conjugation.  This is a good starting point.


On Wed, 10 Oct 2001, David van der Spoel wrote:

> OK, I've attached the pdb file with atoms and residues renamed, for you to
> check.
> What needs doing here is a midified THR and GLY residue in rtp and hdb
> file (THX and GLX or something like that). The THX will not have O, while
> the GLX will not have H. The pdb file residues for THX should be renamed.
> Then you have to make an entry in the specbond file which looks like
> GLY	N	1	THX	C	1	0.138	GLX	THX
> where 0.138 is the bond length
> The only remaing item is the charge, which is probably not very high,
> typically -0.1 for N and 0.1 for C. This will make the residues have
> non-integer charge.
> The final final thing is the improper dihedrals for keeping the ring flat.
> You may have to add these manually. The question is how flat it should
> be....
> 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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