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
Steve
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, December 10, 2020 12:04 PM
To: AMBER Mailing List <amber.ambermd.org>
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.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7Cstevesei%40ku.edu%7C46c1a932ba584034fe2408d89d35f88b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637432202437332003%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=W9hVL5%2BQQRtsq7qbTW7kGkl%2BpkVj2%2BDkILirgRWWMd0%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 10 2020 - 10:30:03 PST
