[AMBER] question for pre-treat protein model

From: Zhuang, Yu <yu.zhuang.tum.de>
Date: Wed, 15 Jan 2014 14:17:27 +0000

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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Received on Wed Jan 15 2014 - 06:30:02 PST
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