AMBER Archive (2004)

Subject: RE: AMBER: Errors when running tleap

From: Bill Ross (
Date: Thu Feb 26 2004 - 13:47:05 CST

> > source
> My file contains the following
> PARM94=loadamberparams frcmod.pcy
> loadAmberPrep cyz.lib
> loadAmberPrep cyd.lib
> 1L1 = loadPdb 1L1O_cys1.pdb
> bond 1L1.481.SG 1L1.500.zn
> bond 1L1.486.SG 1L1.500.zn
> bond 1L1.503.SG 1L1.500.zn
> saveAmberParm 1L1 prmtop.nowat prmcrd.nowat
> I had 3 bond statements in my file.Are the
> following errors? or can i just ignore them
> bond: Argument #1 is type String must be of type:
> [atom]
> usage: bond <atom1> <atom2> [order]

When something is wrong, it is often useful to look at what went
before. Perhaps there were some messages about "1L1 = loadPdb 1L1O_cys1.pdb"?
The 'bond' error message says that 1L1.481.SG does not name anything, which
implies either that 1L1 was not created by the loadPdb statement or that
there are fewer than 481 residues in it, or that the 481st residue does
not have an atom named SG.


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