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

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Tue, 03 Jun 2014 15:19:52 +0530


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 leap.in file.

My leap.in 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


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
C/O Dr. Balvinder Singh
AMBER mailing list
Received on Tue Jun 03 2014 - 03:00:03 PDT
Custom Search