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 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
_______________________________________________ AMBER mailing list AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber [1]
>
> --------------------------------------
> 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
> --------------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [1]
--
Sangita Kachhap
SRF
C/O Dr. Balvinder Singh
BIC
IMTECH
Links:
------
[1] http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 03 2014 - 04:00:02 PDT
