Hi,
Basically I am working ( doing Ph.D ) with Non-natural amino acid and
making peptides using these template. I am doing NMR studies with these
peptides. But we need to do modelling with NMR refinement structure. For
that I need to have force field for these peptide (topology file).Then i
need to simulate these peptide with NOE ( got from NMR NOESY
spectra) restraint. I am trying with AMBER 9 to get force field by
antechamber. I am sucessful to get xxx.prmtop and xxx.incprd file.But i dont
know how to give input topology file into XPLOR-NIH to get energy minimized
structure with NOE refinement.How to give NOE restraint that also i
dont know. If somebody help me what to do and give an example with syntax
(each and every step details), i will be pleased. I am crazy to learn
XPLOR-NIH. But somebody has to help me. I am basically synthesis person,
dificult to understand the programme in a short period.Kindly help me.
--
Anupam Bandyopadhyay
JRF(CSIR),Peptide chemistry
Indian Institue of Science Education and Research
(IISER-Pune) Sai Trinity Building, Garware Circle, Pashan,
Pune, India
Ph. +919370410439
Mail ID: a.bandyopadhyay at iiserpune.ac.in
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