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 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
>
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
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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Received on Tue Jun 03 2014 - 04:00:02 PDT
