Re: [AMBER] question for pre-treat protein model

From: Zhuang, Yu <>
Date: Wed, 15 Jan 2014 14:42:41 +0000

Hi Wei,
Thank you very much for your promote reply. just to make it clear, I should first go to PDB file and delete the H atoms from S. and then modified CYS to CYX in PDB. Is that corrected? Can I use a command to achieve that? (sorry I just new to Amber and it seems there is a lot to learn): )
cheers, Yu

-----Ursprüngliche Nachricht-----
Von: Ye Wei []
Gesendet: Wednesday, January 15, 2014 3:29 PM
An: AMBER Mailing List
Betreff: Re: [AMBER] question for pre-treat protein model

Hi Yu,
This is because the disulfide bond between CYS are not recognized by leap.
Please check the CYS pairs and delete the H atoms on their S atoms (if there are).
In advance, you can modified residue name of the CYS above to "CYX"; Furthermore, you can add "CONECT" info at the end of the pdb file to tell leap the disulfide bonds in the structure.
Hope helps,


At 2014-01-15 22:17:27,"Zhuang, Yu" <> wrote:
>Dear Amber users,
>Currently I am doing the pre-treatment of protein model by Xleap. However, there is an error occurs as following. Did anyone knows how I could solve this problem? I would like to generate a prmtop and inpcrd file for Amber. Many many thanks in advance.
>> saveamberparm unit 2q2m_wat.prmtop 2q2m_wat.inpcrd
>Checking Unit.
>WARNING: The unperturbed charge of the unit: -0.999887 is not zero.
>-- ignoring the warning.
>Building topology.
>Building atom parameters.
>Building bond parameters.
>Could not find bond parameter for: SH - SH Building angle parameters.
>Could not find angle parameter: HS - SH - SH Could not find angle
>parameter: SH - SH - C2 Could not find angle parameter: SH - SH - HS
>Could not find angle parameter: C2 - SH - SH Building proper torsion
>** No torsion terms for HS-SH-SH-C2
>** No torsion terms for HS-SH-SH-HS
>** No torsion terms for C2-SH-SH-C2
>** No torsion terms for C2-SH-SH-HS
>Building improper torsion parameters.
>total 434 improper torsions applied
>Building H-Bond parameters.
>Parameter file was not saved.
>Regards, Yu
>AMBER mailing list

Wei Ye, PhD Candidate
Department of Bioinformatics and Biostatistics, School of Life Science, Shanghai Jiaotong University, Shanghai, China.
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Received on Wed Jan 15 2014 - 07:00:02 PST
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