[AMBER] tleap building a peptide

From: Seibold, Steve Allan <stevesei.ku.edu>
Date: Thu, 10 Dec 2020 16:48:09 +0000

I am attempting to build a peptide using tleap with a disulfide bond. I have no problem making the peptide; however, when I add the CYX to CYX disulfide, I get the error:
> bond mol.4.SG mol.133.SG
bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]

Yet the usage is correct here: mol = name.pdb and the atom numbers are 4 and 133 for SG. The problem maybe that the distance between the CYX atom 4 and the CYX atom 133 is long. I was hoping to generated a strained structure (long distance between atom 4.SG and atom 133.SG )and then minimize to a "real" conformation; but, this may not be possible in AMBER. If so, does anyone have an idea how to do this?

Thanks Steve
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Received on Thu Dec 10 2020 - 09:00:02 PST
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