Thanks Jason,
I am eagerly waiting for the release of the new mmpbsa.py.
In the meantime, it seems to me what you are suggesting is to prepare the
system with the water cap and use the whole thing in the mmpbsa.py turning
off the strip_mdcrd.
I'll give it a try
Rami
On 3/15/11 10:43 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
> MMPBSA.py gives you the flexibility to adjust any input file that is created
> in arbitrary ways (noting that we won't be able to predict errors based on
> your input). The manual details how to use the -use-mdins flag in
> conjunction with the -make-mdins flag in order to do what you're trying to
> do.
>
> For the perl version you'll have to manually edit the
> mm_pbsa_createinput.pm(I think that's the one) package and add those
> variables to the &pb namelist
> of the PB input file.
>
> A highly updated (and much-improved) version of MMPBSA.py is about to be
> released that will make installing and using MMPBSA.py much easier (as well
> as much more flexible).
>
> Hope this helps,
> Jason
>
> On Tue, Mar 15, 2011 at 6:34 AM, Osman, Roman <roman.osman.mssm.edu> wrote:
>
>> Hi Dwight,
>> I'm using the peel version. I didn't know I can do it with the python
>> version.
>> Thanks.
>> Rami
>>
>> Sent from my iPhone
>>
>> On Mar 14, 2011, at 11:28 PM, "Dwight McGee" <dwight.mcgee.gmail.com>
>> wrote:
>>
>>> Are you using the python or perl version of MMPBSA?
>>>
>>> On Mon, Mar 14, 2011 at 11:20 PM, Roman Osman <roman.osman.mssm.edu>
>> wrote:
>>>
>>>> Hi,
>>>> I am trying to calculate MMPBSA with the IVCAP = 1; CUTCAP = 15.0
>>>> I am getting the following message in pbsa_com.1.out:
>>>>
>>>> | Flags:
>>>> cap water should only be run with eneopt=1 and frcopt=0
>>>>
>>>> How do I set these parameters in the input?
>>>>
>>>> Thanks for your help,
>>>> Rami Osman
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>>>
>>>
>>>
>>> --
>>> T. Dwight McGee Jr.
>>> Quantum Theory Project
>>> University of Florida
>>> Graduate Student
>>> dwight.mcgee.gmail.com
>>>
>>> "Problems cannot be solved at the same level of awareness that created
>>> them."
>>> Albert Einstein
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>>
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>
>
Roman Osman
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
Tel: 212-659-8627
Fax: 212-849-2456
e-mail: roman.osman.mssm.edu
http://atlas.physbio.mssm.edu/~osmanlab
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Received on Tue Mar 15 2011 - 08:00:13 PDT
