Hello Amber developers,
When I try to prepare a prmtop and crd file for a pdb (2CRT) the following
error messages occur:
$sleap
[gtkleap]$ source /itc/common/amber/10/amber10/dat/leap/cmd/leaprc.ff99SB
[gtkleap]$ set default fastbld on
[gtkleap]$ ctx = loadpdb ctx.pdb
Warning: there is more than one bond made between two neighbouring residues,
maybe cutoff is too small?
Warning: there is more than one bond made between two neighbouring residues,
maybe cutoff is too small?
Warning: there is more than one bond made between two neighbouring residues,
maybe cutoff is too small?
[gtkleap]$ saveamberparm ctx ctx.prmtop ctx.crd
Error: can't find parameter for bond CT-O
I have manually edited the pdb file and changed the CYS to CYX where
appropriate. I also did not find any CT atoms in the pdb file. I don't know
how to check which residues have multiple bonds therefore I can't get rid of
the warning message. I also tried to change the cutoff for cysteine bonds
from 2.2 angstrom to 2.5 angstrom but I don't think thats what the error
message is about. I am a new user of AmberMD and I would greatly appreciate
any help I can get to fix these errors.
Thanks,
Karan
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Received on Mon Aug 09 2010 - 12:00:05 PDT
