There is no &end at the end of the namelist section. All the group input
follows the namelist; it is not part of it.
----- Original Message -----
From: "Francesco Pietra" <chiendarret.gmail.com>
To: <amber.scripps.edu>
Sent: Saturday, October 25, 2008 12:33 PM
Subject: Re: AMBER: Restraining with PMEMD 10
> Hi:
> Could you please check this (ban) min.in:
>
> Steepest-descent min to eliminate clashes
> &cntrl
> imin=1, maxcyc=3000, ntmin=2,
> cut=10, ntb=1, ntpr=50, ntr=1,
> Title one
> RES 79 100
> END
> Title two
> RES 100 200
> END
> Title three
> Res 200 300
> END
> Title four
> Res 300 340
> END
> Title five
> Res 341
> END
> Weight
> WT 32
> END
> END
> /
>
> ERROR: too many values for NAMELIST variable, unit 5, file
> .../min1.in, line 5, position8. Should it not be basically wrong
> (which I doubt), how many residues are allowed per "Title"?
>
> Thanks
> francesco
>
> On Sat, Oct 25, 2008 at 2:57 PM, Robert Duke <rduke.email.unc.edu> wrote:
>> I believe the relevant appendix was dropped to keep the manual under 50
>> pounds... Look at the amber website, ambermd.org. Then look under the
>> heading "The program package" and follow the link "Amber 8 Manual".
>> Under
>> this select the amber 8 manual again, and open the appendices bookmark.
>> Then
>> go to Appendix B: GROUP Specification.
>> Regards - Bob Duke
>> ----- Original Message ----- From: "Francesco Pietra"
>> <chiendarret.gmail.com>
>> To: "Amber" <amber.scripps.edu>
>> Sent: Saturday, October 25, 2008 5:32 AM
>> Subject: AMBER: Restraining with PMEMD 10
>>
>>
>>> Hope not to be posting what has already been clarified.
>>>
>>>
>>> min1.out:
>>>
>>> Amber 10 SANDER 2008
>>> -------------------------------------------------------
>>>
>>> | PMEMD implementation of SANDER, Release 10
>>>
>>> | Run on 10/25/2008 at 10:58:05
>>>
>>> [-O]verwriting output
>>>
>>> File Assignments:
>>> | MDIN: min1.in
>>> | MDOUT: min1.out
>>> | INPCRD: complex_AA1_POP_BOX.inpcrd
>>> | PARM: complex_AA1_POP_BOX.prmtop
>>> | RESTRT: min1.rst
>>> | REFC: complex_AA1_POP_BOX.inpcrd
>>> | MDVEL: mdvel
>>> | MDEN: mden
>>> | MDCRD: mdcrd
>>> | MDINFO: mdinfo
>>> |LOGFILE: logfile
>>>
>>>
>>> Here is the input file:
>>>
>>> Steepest-descent min to eliminate clashes
>>> &cntrl
>>> imin=1, maxcyc=3000, ntmin=2,
>>> cut=10, ntb=1, ntpr=50,
>>> ntr=1, restraintmask=":79-340, 341"
>>> restraint_wt=32,
>>> /
>>>
>>>
>>>
>>> | ERROR: PMEMD 10 does not support restraint_wt option!
>>> | Please use Amber 6/7 GROUP format instead.
>>> | ERROR: PMEMD 10 does not support restraintmask option!
>>> | Please use Amber 6/7 GROUP format instead.
>>>
>>> Input errors occurred. Terminating execution.
>>>
>>> =============
>>> I was (badly) unable to find a description of "Amber 6/7 GROUP
>>> format". I found a thread alluding to possible bad compilation of
>>> pmemd. The one I used (intel ifort, mkl) was suggested by Ross Walker
>>>
>>> archive:
>>> From: Francesco Pietra <chiendarret.yahoo.com>
>>> Date: Sun Jun 01 2008 - 00:12:12 PDT
>>>
>>>
>>> I used it some time ago quite successfully for production MD on a
>>> parallel NUMA-type machine with dual-opteron 875.. This is the first
>>> time I try with restraints on the same machine and compilation.
>>>
>>> Thanks for indicating where the format of restraining should be, or
>>> what else. As the procedure of restraining with this large system in a
>>> lipidic membrane is quite long, I would like to carry it with pmemd.
>>>
>>> francesco pietra
>>> -----------------------------------------------------------------------
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>>> to majordomo.scripps.edu
>>>
>>
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> -----------------------------------------------------------------------
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Received on Sun Oct 26 2008 - 05:11:13 PDT
