Dear AMBER community,
I want to create .prmtop and .inpcrd files for a protein/retro-inverso
peptide complex. I've read in older posts that there is no need to modify
any amber99sb (or its variants) library to include D-amino acids. However,
when I use regular amino acid names for the D- amino acids in the pdb file
I get errors like:
FATAL: Atom .R<NASN 1>.A<HB1 19> does not have a type.
and warnings like:
WARNING: There is a bond of 4.673348 angstroms between:
------- .R<NASN 1>.A<C 15> and .R<GLU 2>.A<N 1>
and of course tleap fails to generate parameters. Below are the command
lines I issue:
tleap -s -f /home/thomas/Programs/Amber10/dat/leap/cmd/leaprc.ff99SBildn
>loadAmberParams frcmod.ff99SBnmr
>mol = loadpdb complex.pdb
>saveAmberParm mol complex.prmtop complex.inpcrd
Could someone please tell me how to fix these error and warning messages?
thanks,
Thomas
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Received on Sun Dec 02 2012 - 15:00:02 PST
