Re: [AMBER] Could not find angle parameter: S - S - S

From: Sangita Kachhap <>
Date: Tue, 03 Jun 2014 16:25:30 +0530


Thanks Hector

By mistake I did it and was not getting why I am getting this error.
Thanks once again.

On 2014-06-03 16:17, Hector A. Baldoni wrote:

> Hi!
> The error emerge because you are trying to make a S-S- bond between three
> sulfur atoms:
> bond mol.227.SG mol.253.SG
> bond mol.253.SG mol.334.SG
> Greeting,
> Hector.
>> Hello everyone I have to do MD simulation of protein having 9 -S-S- bridge. In original there was 5 missing residue so I have generated coordinate for these residue by Modeller. Now to generate topology file for model, I replaced CYS to CYX also add bond command in file. My file is as follows: source leaprc.ff99SB mol=loadpdb mdl4_1q9h.pdb # Make the disulfide bonds bond mol.19.SG mol.25.SG bond mol.50.SG mol.71.SG bond mol.61.SG mol.67.SG bond mol.135.SG mol.401.SG bond mol.169.SG mol.207.SG bond mol.173.SG mol.206.SG bond mol.227.SG mol.253.SG bond mol.235.SG mol.240.SG bond mol.253.SG mol.334.SG check mol charge mol addions mol Na+ 0 solvateOct mol TIP3PBOX 5 saveamberparm mol mdl4_1q9h.prmtop mdl4_1q9h.inpcrd quit I am getting following error and not able to generate topology file: "Could not find angle parameter: S - S - S" Please anyone help me out. With Regards -- Sangita Kachhap SRF C/O Dr. Balvinder Singh BIC IMTECH
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> --------------------------------------
> Dr. Hector A. Baldoni
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
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Sangita Kachhap
C/O Dr. Balvinder Singh
AMBER mailing list
Received on Tue Jun 03 2014 - 04:00:02 PDT
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