Hi Marek,
AMBMASK is fairly easy to use. The following example should help you:
$AMBERHOME/exe/ambmask -p $AMBERHOME/test/dhfr/prmtop7 -c
$AMBERHOME/test/dhfr/md12.x -out amber -find ':LYS,ALA'
This returns the following:
| New format PARM file being parsed.
| Version = 1.000 Date = 12/30/08 Time = 13:56:31
natom = 22930
nres = 6980
original : ==:LYS,ALA;==
tokenized: ==[:LYS,ALA];==
postfix : ==[:LYS,ALA];==
262 atoms selected
RES 6 7
RES 9 9
RES 19 19
RES 26 26
RES 29 29
RES 32 32
RES 38 38
RES 58 58
RES 76 76
RES 81 81
RES 83 84
RES 106 107
RES 109 109
RES 117 117
RES 143 143
RES 145 145
Which is the old style format for specifying all LYS and ALA residues in
your system.
Then your pmemd input file would look like:
title
&cntrl
...,...,
ibelly=1,
...,
/
Allow the following to move
RES 6 7
RES 9 9
RES 19 19
RES 26 26
RES 29 29
RES 32 32
RES 38 38
RES 58 58
RES 76 76
RES 81 81
RES 83 84
RES 106 107
RES 109 109
RES 117 117
RES 143 143
RES 145 145
END
END
Remember, for belly you are specifying what is ALLOWED to move. This is the
opposite of restraints where you specify what is restrained.
I hope this helps,
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Marek Maly
> Sent: Thursday, November 05, 2009 10:03 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] pmemd vs sander.MPI
>
> Hi Bob,
> thanks a lot for this good news !
>
> Could you please ( if it is not so time consuming ) rewrite
> this two lines using so called "old mask syntax" ?
> (Is this "old mask syntax" described in detail somewhere ?)
>
> ---------------------------
>
> ibelly = 1,
> bellymask=':LGM,WAT',
>
> --------------------------
>
> I assume, that probably only this part: ':LGM,WAT' should be changed
> somehow.
>
> Ross pointed out that the conversion could be done with AMBMASK tool,
> but
> after
> short look in Amber10 manual it is not clear to me, how to use it for
> our
> simple purpose.
> If I understood well AMBMASK is flexible tool to dump some selected
> atoms,
> residui to
> some output file and not just a simple tool for conversion of the mask
> syntax from
> actual to old, but probably it could be used this way as Ross mentioned
> it
> in this connection,
> but would be better to see practical example, how to do this particular
> AMBMASK task.
>
>
> Thank you in advance for any additional comments !
>
> Best
>
> Marek
>
>
>
>
> Dne Thu, 05 Nov 2009 14:35:41 +0100 Robert Duke <rduke.email.unc.edu>
> napsal/-a:
>
> > Yes, pmemd fully supports belly, but with the old mask syntax.
> > Restraints are generally a better choice though, for either sander or
> > pmemd, due to the nature of belly vs. restraints.
> > Regards - Bob Duke
> > ----- Original Message ----- From: "Marek Maly" <marek.maly.ujep.cz>
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Sent: Thursday, November 05, 2009 8:36 AM
> > Subject: Re: [AMBER] pmemd vs sander.MPI
> >
> >
> > Hi Ross,
> >
> > just the short question to this topic.
> >
> > Is it after the proper syntax conversion (as you described below)
> > possible
> > to use PMEMD also in case when part of simulated system
> > is totally froze using ibelly/bellymask approach ?
> >
> > Thanks in advance for your info !
> >
> > Best,
> >
> > Marek
> >
> >
> > Dne Wed, 04 Nov 2009 19:33:23 +0100 Ross Walker
> <ross.rosswalker.co.uk>
> > napsal/-a:
> >
> >> Hi Taufi,
> >>
> >>> I am using sander.MPI to run a dynamics simulation with a restraint
> >>> mask
> >>>
> >>> Molecular Dynamics for 2ns - only Surface atoms are fixed
> >>>
> >>> can i run the above with pmemd by changing the last two lines
> >>> Molecular Dynamics for 2ns - only Surface atoms are fixed
> >>
> >> Yes. PMEMD just needs the old restraint syntax. There is a tool
> called
> >> ambmask in $AMBERHOME/exe/ which will convert an AMBER mask into the
> old
> >> group format for you.
> >>
> >>> Also, i do remember talking with Dr. Walker about pmemd being
> faster
> >>> and
> >>> just as accurate as sander.MPI, is that also true when using 32 or
> 64
> >>> processors, or is it especially true when using large number of
> >>> processors?
> >>
> >> It will be a LOT faster. If you are running simulations within
> PMEMD's
> >> feature set you should probably always use it since it will be
> faster
> >> even
> >> on 1 processor. On 32+ it will make a big difference. You should be
> >> seeing
> >> performance equivalent to the following (this was run with pmemd)
> >>
> >> http://teragrid.org/userinfo/aus/amber_benchmark.php
> >>
> >> All the best
> >> Ross
> >>
> >>
> >> /\
> >> \/
> >> |\oss Walker
> >>
> >> | Assistant Research Professor |
> >> | San Diego Supercomputer Center |
> >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> >> | http://www.rosswalker.co.uk | PGP Key available on request |
> >>
> >> Note: Electronic Mail is not secure, has no guarantee of delivery,
> may
> >> not
> >> be read every day, and should not be used for urgent or sensitive
> >> issues.
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> __________ Informace od NOD32 4051 (20090504) __________
> >>
> >> Tato zprava byla proverena antivirovym systemem NOD32.
> >> http://www.nod32.cz
> >>
> >>
> >
> >
> >
>
>
>
> --
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Received on Thu Nov 05 2009 - 10:30:05 PST
