AMBER Archive (2009)

Subject: Re: [AMBER] atom numbers

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Tue Apr 21 2009 - 11:58:41 CDT

Dear Dr. david case I am following the sustiva tutorial...bt couldnt get the result......... i checked in my PDB and found out that indeed there are a few atom names which are same..i have attached the Mol2 file of the ligand and that of the protein ligand complex.... please just check.... ________________________________ From: David A. Case <case_at_biomaps.rutgers.edu> To: AMBER Mailing List <amber_at_ambermd.org> Sent: Tuesday, 21 April, 2009 9:22:22 PM Subject: Re: [AMBER] atom numbers >         "source leaprc.ff03 >         source leaprc.gaff >         com = loadpdb 'prot-ligand complex.pdb' > > it gave the result as: > >         residue 317:duplicate [c] atoms (total 2) >         residue 317:duplicate [o] atoms (total 4) >         warning: atom names in each residue should be unique. > (same-name atom are             handled by using the first > occut=rence and by ignoring the rest. You have to fix this in the pdb file: atom *names* (not numbers!) in each residue must be unique. >         Unknown residue: M_$ no:221 type:terminal/last >         Creating a new unit for residue : M_4 sequence:317 >         Created a new atom name:C in residue:.R<M_4 317> Your pdb file has a residue named "M_4", but LEaP has no idea what this means.  See tutorial B4 for an introduction on how to handle non-standard residues. ....dac _______________________________________________ AMBER mailing list AMBER_at_ambermd.org http://lists.ambermd.org/mailman/listinfo/amber On Tue, Apr 21, 2009, Vikas Sharma wrote: >         Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/

  • application/octet-stream attachment: 1.mol2


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