Re: [AMBER] tleap building a peptide

From: Seibold, Steve Allan <>
Date: Thu, 10 Dec 2020 18:11:02 +0000

Thanks for the help! I should have paid more attention to the manual than the error message. I thought the error message was saying it wanted the atom number and not the name.

With that correction, tleap is building the structure correctly...thanks again


-----Original Message-----
From: David A Case <>
Sent: Thursday, December 10, 2020 12:04 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] tleap building a peptide

On Thu, Dec 10, 2020, Seibold, Steve Allan wrote:
>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]

Use the "desc" command to see what you have, e.g. 'desc mol.4' will show you what is in residue 4. See if there is an SG atom there.

>Yet the usage is correct here: mol = name.pdb and the atom numbers are
>4 and 133 for SG.

The second part of 'mol.4.SG' is the *residue* number, not the atom number.

The problem maybe that the distance between the CYX
>atom 4 and the CYX atom 133 is long.

No: tleap will create a bond without looking at the distance. You problem is the "mol.4.SG" does not refer to any atom that tleap knows about.


AMBER mailing list;;sdata=W9hVL5%2BQQRtsq7qbTW7kGkl%2BpkVj2%2BDkILirgRWWMd0%3D&amp;reserved=0

AMBER mailing list
Received on Thu Dec 10 2020 - 10:30:03 PST
Custom Search