AMBER Archive (2008)

Subject: Re: AMBER: Restraining with PMEMD 10

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Oct 25 2008 - 13:57:40 CDT

Hi Ross:
One should not forget about your tutorials!

Conjugated gradient minimization
&cntrl
  imin=1, maxcyc=3000, ntmin=0,
  cut=10, ntb=1, ntpr=50, ntr=1
/
Keep protein and ligand fixed
32.0
RES 79 341
END
END

gave no errors with pmemd (I had run steepest descent min with sander).
===

During heating and first dynamics, I want to keep restrained also the
polar heads of POPC lipid. With sander.MPI that would be

restraintmask="79-341 | :POP_at_O2, P1, O3, O4, O1, C15, C11, N, C12, C13, C14"
restraint_wt=32,
nmropt=1

Is it any example of restraining atoms with GROUP in the tutorials? If:

Keep protein, ligand and POPC head fixed
32.0
Title one
RES 1 78
END
Title two
ATOM ???
Title three
RES 79-341
END
END

where 1-78 are POPC, 341 ligand, and the rest protein. From the
ambmask pdb for the input complex I can read atom numbers but the are
many repeating POPC units. I must be completely on a wrong way.
Thanks
francesco

I can read the atom numbers for POPC from the ambmask pdb file for the
complex protei-ligand in a box, but there are many POPC units

On Sat, Oct 25, 2008 at 7:25 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Francesco,
>
> The group specs go after the / of the cntrl namelist. See tutorial B1 for an example:
>
> http://ambermd.org/tutorials/basic/tutorial1/section5.htm
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Francesco Pietra
>> Sent: Saturday, October 25, 2008 9:34 AM
>> To: amber_at_scripps.edu
>> 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_at_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_at_gmail.com>
>> > To: "Amber" <amber_at_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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>> >
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