AMBER Archive (2006)

Subject: Re: AMBER: PMEMD with NMR restraint and position restraint

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Jul 18 2006 - 21:03:42 CDT

Ting -
I am copying to the amber mailing list because UC Davis is blocking mail
coming from roadrunner. The reason I modify pmemd code is because I am the
developer (so I am also interested in detecting/fixing any bugs, and will
issue patches in this release and fix the code for the next release if it is
broken). The part of it you are having trouble with I don't actually use
or have test cases for, so that is why there can be a problem I don't know
about. Could you perhaps make a gzipped tarball of all your run files that
are not working (prmtop, inpcrd, mdin, any redirected inputs) as well as a
shell script with your command line and send it to me. I can then do a
little test work with your system as input. I treat all files I get like
this as confidential. Sorry
for the grief, but I will get it working for you.
Regards - Bob Duke

----- Original Message -----
From: "Ting Wang" <twang_at_ucdavis.edu>
To: <rduke_at_email.unc.edu>
Sent: Tuesday, July 18, 2006 8:06 PM
Subject: Re: AMBER: PMEMD with NMR restraint and position restraint

> Hi Bob,
>
>> I am not an expert on the various stuff that can come after the
>> namelists, but I believe if you delete line 15 from the mdin (an END
>> "card"), your mdin should work.
>
> I tried, but this did not work.
>
>> If not, then I have managed to break the code sometime over the last year
>> or two in regard to this issue. Please let me know, either way. The
>> code does not expect an END card following file redirections, as far as I
>> can tell.
>
> Do you mean you have a modified PMEMD code?
>
> Thanks,
>
> Ting
>> Regards - Bob Duke
>>
>> ----- Original Message -----
>> From: "Ting Wang" <twang_at_ucdavis.edu>
>> To: "Robert Duke" <rduke_at_email.unc.edu>; <amber_at_scripps.edu>
>> Sent: Tuesday, July 18, 2006 4:12 PM
>> Subject: Re: AMBER: PMEMD with NMR restraint and position restraint
>>
>>
>>> Hi Bob,
>>>
>>> Here is my input file, I also tried to put the nmr restraint part after
>>> the
>>> positional restraint part.
>>>
>>> Thank you very much!
>>>
>>> Ting
>>>
>>>> Ting -
>>>> Exactly what does your input mdin file look like? I believe pmemd
>>>> takes a
>>>> subset of the possibilities for specifying both nmr and positional
>>>> restraints; I have not tried to fix this code to accept all
>>>> possibilities
>>>> because the exact definition of "all possibilities" has been a poorly
>>>> specified moving target. Anyway, if you show us exactly what you did,
>>>> we
>>>> can probably propose alternatives that work (folks that do this
>>>> routinely,
>>>> please jump in; I don't have a good test case myself).
>>>> Regards - Bob Duke
>>>> ----- Original Message -----
>>>> From: Ting Wang
>>>> To: amber_at_scripps.edu
>>>> Sent: Monday, July 17, 2006 7:18 PM
>>>> Subject: AMBER: PMEMD with NMR restraint and position restraint
>>>>
>>>>
>>>> Hi,
>>>>
>>>> I am running PMEMD/amber9. I need to set both NMR distance restraints
>>>> (nmropt=1) and position resstraints (ntr=1). But I found PMEMD can work
>>>> with either restraint type alone but not both together.
>>>>
>>>> Any suggestion?
>>>>
>>>> Thanks,
>>>>
>>>> Ting
>>>
>>
>>
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>
>

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