AMBER Archive (2005)

Subject: Re: Re: AMBER: radius parameter for F atom

From: Ye MEI (ymei_at_itcc.nju.edu.cn)
Date: Tue Apr 26 2005 - 08:30:07 CDT

Dear Junjun,

Thank you for your reply, but I do set RADIOPT=0.

Ye MEI
        

======= 2005-04-26 09:36:16 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>Dear Ye:
>
>I think you can try "RADIOPT=0".
>
>A value of 0 uses the cavity radii from the prmtop file. A value of 1 sets
>up optimized cavity radii at the pbsa initialization phase.
>
>On Tue, 26 Apr 2005 01:05:06 +0800, Ye MEI <ymei_at_itcc.nju.edu.cn> wrote:
>
>> Dear Amber Users,
>>
>> I am trying mm_pbsa to calculate the binding free energy of a ligand
>> containing F atoms to a peptide. I set PROC=2, so pbsa in amber8 is used
>> to analysis the trajectory, instead of delphi. I guess amber should read
>> charge and radius parameters from prmtop file. But the pbsa failed with
>> an error message as following:
>> Calc MM/GB/SAS
>> Generate PDB
>> Center PDB
>> Calc PBSA
>> Generate PQR
>> No radius found for F1 15606 in residue EFZ 946
>> I am sure the prmtop file contains the radii parameters for all the
>> atoms including F atoms. So I cannot think out why this error is
>> encountered. Will anyone oblige me with the solution to this failure?
>>
>>
>> Ye MEI
>> ymei_at_itcc.nju.edu.cn
>> 2005-04-26
>>
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>
>
>
>--
>JunJun Liu
>
>College of Chemistry
>Central China Normal University
>WuHan 430079
>P.R. China
>
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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Ye MEI
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ymei_at_itcc.nju.edu.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-04-26

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