AMBER Archive (2009)

Subject: Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz

From: Manish Kumar (kumarmanish.amb_at_gmail.com)
Date: Sun Jul 19 2009 - 14:36:35 CDT

Dear Prof. Ray,

 I was trying to use DElPHI because of two reasons,
 First, some papers say that the pbsa module of Amber is not consistence
with the DELPHI results, but it may be true for older version.
 Second, I have learned from on the internet that pbsa module can not be
used for charged ligand. I don't know how true it is with Amber10.

However, I tried doing mm-pbsa using pbsa module of Amber and I am getting
following error.

.........................
........................
    Processing PB PBTOT
        Doing 1 PB PBSOL
        Doing 1 MM GAS
    No values for MM_GAS existing -> Skipping
    Processing MM GAS
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
    Processing PB PBTOT
        Doing 1 PB PBSOL
        Doing 1 MM GAS
        Doing 1 PB PBSOL
        Doing 1 MM GAS
        Doing 1 PB PBSOL
        Doing 1 MM GAS
=>> Calc delta from raw data
    No data for 0+0 MM BOND 0

I will applicate any help.

Sincerely,
Manish

On Fri, Jul 10, 2009 at 12:32 PM, Ray Luo <ray.luo_at_uci.edu> wrote:

> Is there any compelling reason that you cannot use PBSA in Amber10? Note
> that PBSA is numerically consistent with Delphi given exact input
> coordinates and coordinates. If you want to use Delphi, you are on your own
> because we no longer offer developer support to Delphi in Amber.
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
>
> Manish Kumar wrote:
>
>> Dear Experts,
>> I am still waiting for the guidance. I searched in Google, as well as
>> mailing archive but didn't get the answer.
>>
>> On Wed, Jul 8, 2009 at 5:29 PM, Manish Kumar <kumarmanish.amb_at_gmail.com
>> >wrote:
>>
>>
>>
>>> Hi,
>>> I am trying to do mm-pbsa calculation in Amber10. How can I create
>>> delphi.crg
>>> and delphi.siz for my system.
>>>
>>> Thanks!
>>>
>>>
>>>
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>>
>>
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