Re: [AMBER] tleap building a peptide

From: Seibold, Steve Allan <>
Date: Thu, 10 Dec 2020 18:03:33 +0000

Thanks for the response...
My peptide is 16 residues long with NCYX and CCYX at termus
My input is:

source leaprc.protein.ff14SB
mol = loadpdb GBP_noH.pdb
bond mol.8.SG mol.10.SG
savepdb mol GBP.pdb
saveamberparm mol GBP.prmtop GBP.inpcrd
when I run desc mol.1, I get the SG atom is number 10
when I run desc mol.16 I get the SG atom is number 8

However, I still get the error:

bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
Writing pdb file: GBP.pdb
 Converting N-terminal residue name to PDB format: NCYX -> CYX
 Converting C-terminal residue name to PDB format: CCYX -> CYX
Checking Unit.

Thanks Steve

-----Original Message-----
From: Carlos Simmerling <>
Sent: Thursday, December 10, 2020 11:09 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] tleap building a peptide

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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