Re: [AMBER] tleap building a peptide

From: Carlos Simmerling <>
Date: Thu, 10 Dec 2020 12:08:34 -0500

length shouldn't matter.
try "desc mol" to check the atom numbers.

On Thu, Dec 10, 2020 at 11:48 AM Seibold, Steve Allan <>

> 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 - 09:30:02 PST
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