> 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?
You could look at the model in xleap after loadpdb and see if
any bonds are inappropriate. It is too bad that the warning msg
does not mention which residues.
I think the ability to add multiple bonds on loadpdb has been
added since my own work on leap, so can't comment more.
> [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.
> I also did not find any CT atoms in the pdb file.
That's the atom type - only atom names appear in pdb.
What parm.dat and frcmod files are you loading? These are
where all force field parameters except atomic charges come from.
Bill
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Received on Mon Aug 09 2010 - 12:30:03 PDT
