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 - 15:49:05 CDT

Ting -
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. 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.
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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