Fabien -
There are two basic groups of restraints. You get coordinate positional
restraints by setting ntr to 1 and defining a group. That is what was done
here. In this file, nmropt was also set to 1 in order to be able to do
temperature weight changes. Now, there are also other things one can do
under the category of "restraints". It is possible to specify distance,
angle and torsion restraints by setting nmropt to 1 and including one or
more &rst namelists. THIS is what the code is talking about not finding.
There are also NOESY and chemical shift restraints that one can get by
setting nmropt to 2 and doing a few other things in sander. PMEMD does not
support these and will do a "halt and catch fire" if you specify nmropt = 2.
Just to add another layer of potential confusion, sander 8 also now supports
a new input format for positional restraints which is simpler than group
input; there is an example on page 93 of the amber manual. PMEMD DOES NOT
YET support this new format; you have to use the old group stuff, but that
seems to be what most folks do anyway.
Bob Duke
----- Original Message -----
From: "Fabien Cailliez" <Fabien.Cailliez.ibpc.fr>
To: <amber.scripps.edu>
Sent: Thursday, January 27, 2005 4:01 AM
Subject: Re: AMBER: pmemd and restraints
> Dear all,
> I had the same problemas Dr Lankas.
> It seems that for pmemd from AMBER8 (as well as for sander I suppose), the
> restraints have to be put under
> the heating stuff, in contrary to what was done in sander from AMBER7.
> I am not sur about that but when I placed restraint informations at the
> end, pmemd did not complain.
> However, there is a strange message in my mdout file, saying that no
> restraint was defined, despite the fact that these restraints
> have been read correctly before, and that RESTRAINT energy is not zero
> during the simulation.
> Here is the part of the mdout file with thses information :
>
> 5. REFERENCE ATOM COORDINATES
>
> ----- READING GROUP 1; TITLE:
> Group input for protein restraints: 25 kcal/mol.
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 25.00000
> GRP 1 RES 1 TO 442
> Number of atoms in this group = 6620
> ----- END OF GROUP READ -----
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> begin time read from input coords = 0.000 ps
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> TEMP0 0 5000 100.000000 300.000000 0 0
> TEMP0 5001 25000 300.000000 300.000000 0 0
>
> RESTRAINTS:
> No valid redirection requests found
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
> Does anyone know what this last message is for ?
> Thank you in advance,
> Fabien
>
> Filip Lankas wrote:
>
>>
>> Hello Amber users,
>>
>> I have a problem running pmemd with position restraints and increasing
>> temperature. The system is a piece of DNA with explicit ions and water,
>> periodic, PME. My input file looks like this:
>>
>>
>> Group input for DNA restraints: 25 kcal/mol.
>> 25.0
>> RES 1 24
>> END
>> END
>> ***************************** md.in *****************************
>> *************************************************************************
>> Heating the system with 25 kcal/mol restraints on DNA, V=const
>> &cntrl
>> imin=0, ntx=1, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
>> nscm=5000,
>> ntf=2, ntc=2,
>> ntb=1, ntp=0,
>> nstlim=50000, t=0.0, dt=0.002,
>> cut=9.0,
>> tempi=100.0, ntt=1,
>> ntr=1, nmropt=1,
>> lastist=10000000
>> &end
>> Heating from 100 to 300 K
>> &wt type='TEMP0', istep1=0, istep2=5000, value1=100.0, value2=300.0,
>> &end
>> &wt type='TEMP0', istep1=5001, istep2=50000, value1=300.0, value2=300.0,
>> &end
>> &wt type='END', &end
>>
>> ... the job starts, but crashes saying (in the stderr):
>>
>> lib-4001 : UNRECOVERABLE library error
>> Encountered during a sequential formatted READ from unit 5
>> Fortran unit 5 is connected to a sequential formatted text file: "md.in"
>> Current format: 9208 FORMAT(20a4)
>>
>> Am I doing something wrong, or does pmemd simply not support this kind of
>> task?
>>
>> Thank you in advance,
>>
>> Filip
>
>
>
> --
> __________________________________________________________________
> Fabien Cailliez Tel : 01 58 41 51 63 Laboratoire de Biochimie Théorique
> e-mail : cailliez.ibpc.fr
> IBPC 13, rue Pierre et Marie Curie 75005 Paris
> __________________________________________________________________
>
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Received on Thu Jan 27 2005 - 13:53:00 PST
