AMBER: Re: (瑞星提示-此邮件可能是垃圾邮件)Re: AMBER: Can GB and MS work correctly together in mmpbsa?

From: <zhli_2000.126.com>
Date: Tue, 19 Jul 2005 09:23:39 +0800

Hi, Scott
The modification is attached by the mm_pbsa_calceneent.pm file. Please
check it and tell me whether I do it correctly.
It seems that using MS=1 the programm can read the parameter of atom F from
the mm_pbsa_calceneent.pm file. But only using GB=1 and MS=0, there is no
parameter of atom F to be read, even if mm_pbsa_calceneent.pm file has been
added the radium of atom F.
So what should I do to deal with this ?




On Mon, 18 Jul 2005 11:31:29 -0600, Scott Pendley <scott.pendley.gmail.com>
wrote:

> Why don't you email me directly and show me what modifications you
> have done to the code to account for Fl. This is a tricky problem and
> you make need some hands on assistance with this.
>
> On 7/16/05, zhli_2000.126.com <zhli_2000.126.com> wrote:
>> Thank you for the advice. I have put the atom radium of F in the
>> mm_pbsa_calceneent.pm. Then I run the following :
>>
>> --------------------------------------------------------------------
>> PREFIX min_cyc16
>> PATH ./
>> #
>> COMPLEX 1
>> RECEPTOR 1
>> LIGAND 1
>> #
>> COMPT ./mincomplex.top
>> RECPT ./ppo.top
>> LIGPT ./cyc16.top
>> #
>> GC 0
>> AS 0
>> DC 1
>> #
>> MM 1
>> GB 1
>> PB 0
>> MS 0
>> #
>> NM 0
>> #
>> -------------------------------------------------------------------
>> The error message is still :
>> bad atom type: F
>>
>> When I switch MS=0 to MS=1, the error message is:
>> Checking sanity
>> Checking GENERAL
>> Energy decomp is not (yet) possible with GC, AS, NM, PB, MS
>>




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Received on Tue Jul 19 2005 - 02:53:00 PDT
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