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

From: 126 <yw20055968.126.com>
Date: Wed, 15 Jan 2014 22:51:19 +0800

Actually,I think the first step could work. As AMBER could transfer CYS to CYX if these 2 CYS don't have H on S and they are enough close.
If not, go to the other two steps.

And one more thing, you need add one Na+ to keep the system neutral.

Best,

Wei Ye
PhD Candidate
Department of Bioinformatics and Biostatistics,
School of Life Science and Technology,
SJTU

ď┌ 2014-1-15úČ22:42úČ"Zhuang, Yu" <yu.zhuang.tum.de> đ┤Á└ú║

> 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
>
> -----UrsprĘ╣ngliche Nachricht-----
> Von: Ye Wei [mailto:yw20055968.126.com]
> 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,
> Best,
> Wei.
>
>
>
>
>
>
>
>
> At 2014-01-15 22:17:27,"Zhuang, Yu" <yu.zhuang.tum.de> 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
>> parameters.
>> ** 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
>>
>> _______________________________________________
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>
>
>
>
>
>
>
> --
>
> Wei Ye, PhD Candidate
>
> Department of Bioinformatics and Biostatistics, School of Life Science, Shanghai Jiaotong University, Shanghai, China.
> Email: yw20055968.126.com
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Received on Wed Jan 15 2014 - 07:00:03 PST
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