Hi,
> There is a zinc ion in my protein system ,the Zinc is bond to
> three amino acids and one water (His ,HIs ,GLU ,H2O).Now ,the model
> of zinc was extrated from the crystal structure.The Glu was
> truncated into butyrate,the HIS is also trncated as R-CH3(I changed
> the -NH2-CHR-CO to R-CH3).Geometry optimization were carried out
> using Gaussian. I have got the parameters,such as bond,resp
> charge....My question is : How should I deal with the residues if I
> write the lib file ?
You need to create a FF library in the .mol2, prep or off file format.
The advantages of the mol2 file format is that it can be used as a FF
lib in LEaP but also visualized in graphical programs such as VMD...
The idea of a FF library is that the atom & residue names in this FF
library have to match these in the PDB file (i.e. the crystal
structure). You load all the FF libs in LEaP & then the PDB file, and
LEaP will do the job of recognition between the FF libs & the PDB file.
An another important point is that two toms belonging to the same
residue in a FF library cannot bear the same name; otherwise LEaP will
complain (while VMD accepts this option).
Thus, often this better to think how to integrate the FF lib in a
biopolymer before to compute the charges. Moreover, you have to define
the topology you wish to set up in your bioinorganic complex (presence
of atom connectivities or not).
If you use R.E.D. a Tripos mol2 file is generated as a final output;
the topology/atom names/residue names are defined in the p2n input
file before the charge derivation step. Then, you need to define the
FF atom types and you simply load all in LEaP.
regards, Francois
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Received on Fri May 21 2010 - 23:00:03 PDT
