AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa energy decomposition error

From: amit_at_mbu.iisc.ernet.in
Date: Thu Aug 25 2005 - 06:57:18 CDT


Hi Dac,
       Finally I got the energy using the flag gbsa=0. But the program is
stopped when getting to statistical part. The error I got

 Reading files
    Reading 1pfy_com.all.out
    Reading 1pfy_rec.all.out
    Checking CALC
    Reading 1pfy_lig.all.out
    Missing SINT for MM in 1 (residue 1)
Please help.
Another problem by putting gbsa=0, which is used for stopping the
solvent-accessible surface area calculation within sander.In order to
calculate the same I have included parameters for zinc in mdread.f. But
that doesnt solve the problem.
Any hint.

Sincerely,
amit

> On Wed, Aug 24, 2005, amit_at_mbu.iisc.ernet.in wrote:
>>
>>
>> I am using amber8 to calcuate binding energy of
>> protein/ligand system. Satibility and binding calculation
>> is working fine. But I got "bad atom type: ZN" when I run
>> energy decomposition. I used leap to generate lib & frcmod
>> files for Zn which is part of complex.
>> I dont know what went wrong.
>
> Use the Google search bar on the Amber web page, and search for "bad atom
> type" in the mailing archives. This will give you lots of information.
>
> The simplest workaround will be to set gbsa=0.
>
> ...good luck...dac
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