AMBER Archive (2005)

Subject: Re: AMBER: Can GB and MS work correctly together in mmpbsa?

From: Alfonso Garcia-Sosa (atg21_at_hermes.cam.ac.uk)
Date: Mon Jul 18 2005 - 14:16:21 CDT

I believe you also might need to add the radius of F in the
my_parse_delphi.siz file, included in the amber distribution.

Alfonso Garcia-Sosa

On Mon, 18 Jul 2005, Scott Pendley 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_at_126.com <zhli_2000_at_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
>>
>> So I don't know how to deal with this. Which input file can be run
>> correctly?
>>
>> ----------------------------------------------------------------------------
>> ---
>>
>> On Fri, 15 Jul 2005 14:08:43 -0600, Scott Pendley <scott.pendley_at_gmail.com>
>> wrote:
>>
>>> As a follow up to my last note. Specifically you should modify the
>>> generate_pqr() section of mm_pbsa_calceneent.pm. This is the
>>> modification I added to my code . . .
>>>
>>> "Na+" => 1.200 + 1.400,
>>> "Cl-" => 1.700 + 1.400,
>>> "MG" => 1.180 + 1.400,
>>> "F" => 1.470 + 1.400,
>>> );
>>>
>>> Have fun with this...
>>>
>>>
>>> On 7/15/05, Scott Pendley <scott.pendley_at_gmail.com> wrote:
>>>> That is because you have not put in the parameters of F for the
>>>> molsurf program. It is similiar to doing to the modification you did
>>>> earlier. If you run into trouble doing this let me know and I will
>>>> show you how I did it.
>>>>
>>>> On 7/15/05, zhli_2000_at_126.com <zhli_2000_at_126.com> wrote:
>>>>> Hi,
>>>>> Thank you for the explanation. But Because there is an atom F in the
>>>>> ligand, when I switch MS=1 to MS=0, mmpbsa cann't work correctly. The
>>>> error
>>>>> message is:
>>>>> bad atom type: F
>>>>>
>>>>> What should I do?
>>>>> Thank you!
>>>>>
>>>>>
>>>>>>
>>>>>> If you switch MS=1 to MS=0, it should work. Energy decomposition
>>>> does not
>>>>>> work so far with a SAS calculation based on MS, but relies on
>>>> another
>>>>>> method approximating atomic surfaces starting from icosahedra.
>>>>>> Best regards
>>>>>>
>>>>>> Holger
>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>
>>>>
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>>
>>
>>
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