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Hello Anupam-- > 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. There are basically two ways to introduce non-natural amino acids: 1) if it's a simple modification of an existing residue (like phosphorylation) you can patch the existing residue- and writing a patch can be fairly easy - see examples in toppar/protein.top in the Xplor-NIH distribution (search for presidue). 2) if it's not a simple modification, it's probably best to create a new residue type. You can have the prodrg server (http://davapc1.bioch.dundee.ac.uk/prodrg/) help with this, but there's usually a fair amount of manual manipulation. I am happy to help in this process- doing this will force me to eventually automate the process. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkvtlrkACgkQPK2zrJwS/lZx0QCfUOEc0JXiKssHGODgj/5pVu5T PWIAn1RnCUQU5EDczX+5vf77UBRQPOyY =jcSr -----END PGP SIGNATURE-----
