[gmx-users] position restraint on crystal water
Dilraj Lama
dennis at iitk.ac.in
Thu Jul 14 15:30:40 CEST 2005
Thanks again David,
But I have tried that also. I have included the statement
[ position_restraints ]
1 1 1000 1000 1000
(as you have suggested)
after the hoh.itp file (for crystal water), but it restrains all the crystal water molecules and
not only the crystal water of my intrest as I am intrested to restrain only some of the crystal
water and not all.
Also in this case grompp gives me a new error.
number of coordinates in coordinate file (out.gro, 96613) <-- out.gro produced by genbox program
does not match topology (*.top, 96982)
I suspect the reason for this error is that when genbox program produces the out.gro file it also
counts crystal water as a solvent so that the number of atoms in out.gro files is actually less by
369 (123*3=369) atoms. So i subtracted the number of SOL molecule in *.top file by 123., then it
works fine. is it is the correct way to do that ?????? or i did wrong?????
But my first problem hstill exists i.e. "HOW CAN WE APPLY POSTION RESTRAIN ON SELECTED CRYSTAL
WATER MOLECULES"??????????
I am very much thankfull for your kind help.
Regards,
Dilraj Lama
----- Original Message -----
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, July 14, 2005 1:57 PM
Subject: Re: [gmx-users] position restraint on crystal water
> On Thu, 2005-07-14 at 11:41 +0530, Dilraj Lama wrote:
> > Hello David,
> > Thanks again, and sorry to bother you again.As you
pointed-out in the last mail ,I
> > checked my *.top file and i found that i had put the position restrain
for crystal water water at
> > wrong place,so i corrected it but even then i am facing similar error
but the error message is
> > different now :
> >
> > Fatal error: [ file "posre_cryst_water.itp", line 8 ]:
> > Atom index (2042) in position_restraints out of bounds
(1-3)
> >
> > I am also pasting the section of my *.top file
> >
> > SECTION OF MY *.TOP FILE
> > ************************
> >
> > ; Include Position restraint file for selected residues of protein
> > #ifdef POSRES_SELECT_PROTEIN
> > #include "posre_select_protein.itp"
> > #endif
> >
> > ; Include crystal water topology
> > #include "hoh.itp"
> >
> > ; Include Position restraint file for crystal water
> > #ifdef POSRES_CRYST_WATER
> > #include "posre_cryst_water.itp"
> > #endif
> In above it should say:
> [ position_restraints ]
> 1 1 1000 1000 1000
>
> >
> > ; Include water topology
> > #include "spc.itp
> >
> > [ system ]
> > ; Name
> > Protein in water
> > [ molecules ]
> > ; Compound #mols
> > Protein 1
> > HOH 123
> > SOL 31533
> >
> > ********************************************************
> >
> > I am also attachig my hoh.itp,
posre_select_protein.itp,posre_cryst_water.itp and em.mdp
> > files along this mail.
> >
> > PS: This time i have named crystal water as HOH (instead of SOLA as in
the previous
> > case)and
> > crystal water itp file as "hoh.itp" (instead of "spcA.itp" as in the
previuos case)
> > file, sorry
> > for the inconvenience
> >
> > I am stuck at this point only , your suggestion can helped me to
overcome this
> > situtaion.
> >
> > Thanks
> >
> > Warm regards,
> > Dilraj Lama
> >
> > > On Wed, 2005-07-13 at 20:11 +0530, Dilraj Lama wrote:
> > >> Hello David,
> > >> Thanks for your promt reply.But i have not so well
understood how to
> > do that.I want
> > >> to apply positions restrain only for selected crystal water molecules
not for all.
> > >>
> > >> So as you suggested I ran pdb2gmx and then renamed SOL
to SOLA in
> > the end of the
> > >> *.top file generated. I also copied spc.itp file in my working
directory and changed
> > >> molecule name SOL to SOLA and renamed the spc.itp file as spcA.itp.I
also renamed
> > all
> > >> the HOH residues (crystal water) in *.gro file (produced by pdb2gmx)
to SOLA before
> > >> running the editconf.
> > >>
> > >> I also included this spcA.itp file in *.top file.then i
ran the
> > editconf & genbox
> > >> program both works fine.but when i tried to run grompp program i got
same error
> > >> message:
> > >> "Atom index (2042) in position_restraints out of bounds (1-2014)".
> > > atom index should be 1-2014 for protein
> > > or 1 for water
> > >
> > > take care that you put the [ position_restraints ] section in the
right
> > > place (i.e. in the spcA.itp file).
> > >
> > >>
> > >> I also tried supplying the default index file to "grompp"
program
> > having a seperate
> > >> group for crystal water ( with name SOLA).But this also produced the
same error.
> > >>
> > >> can you pointout my mistake where i am going wrong.
> > >>
> > >> thanks.
> > >>
> > >> > On Wed, 2005-07-13 at 10:55 +0530, Dilraj Lama wrote:
> > >> >> Hello Everyone,
> > >> >> This is my second post on the same topic.I posted
the query
> > last week but no
> > >> one
> > >> >> has responded.Any suggestion or thought would be of great help to
me.
> > >> >>
> > >> >> I know this topic has been discussed several times in the
mailing list
> > but i am
> > >> >> still not very clear and as a result am not able to find any
solution to my
> > problem.
> > >> >>
> > >> >> I am presently trying to do simulation of a
Protein which
> > alsohave crystal
> > >> >> waters.I don't want to remove these water molecules.so after
solvation of the
> > >> >> proteinin water, my system looks like :-
> > >> >>
> > >> >> [ molecules ]
> > >> >> ; Compound #mols
> > >> >> Protein 1
> > >> >> SOL 123 <----Crystal Water
> > >> >> SOL 31472
> > >> >>
> > >> >> Now i am trying to do minimization of my solvated system by
applying position
> > restraint on
> > >> two
> > >> >> crystal water and two residue of the protein. but when i try to
preprocess my
> > inputfiles
> > >> using
> > >> >> "grompp" program,i get the following error message:
> > >> >>
> > >> >> "Atom index (2042) in position_restraints out of bounds (1-2014)".
> > >> >>
> > >> > you've used the wrong atom index. presumable 2042 is a water,
however
> > >> > you need to restrain atom 1 of the water.
> > >> >
> > >> > if you only want to restrain some of the waters you will have to
make
> > >> > two solvent molecule definitions (i.e. copy spc.itp to spca.itp and
> > >> > rename the molecule to SOLA and restrain only those). Do also check
> > >> > chapter 5.
> > >> >
> > >> >
> > >> >> note:2014 is the last atom number of the protein in the ".gro"
file.
> > >> >>
> > >> >> I also tried to do the same after changing the name of crystal
water from SOL
> > to SOLA but it
> > >> >> also
> > >> >> dosen't work.
> > >> >>
> > >> >> Any suggestions/comments are most wellcome
> > >> >>
> > >> >> Thanks In advace.
> >
> >
> > --
> > Dilraj Lama,
> > PhD Student,
> > c/o Dr. R. Sankararamakrishnan,
> > Bioinformatics and Biomolecular Simulation Lab,
> > Dept. of BSBE,IIT-Kanpur,
> > UP-208016:India
> > email:dennis at iitk.ac.in;dilraj2002 at yahoo.com
> > mob:09415473973
> > _______________________________________________ gmx-users mailing list
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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--
Dilraj Lama,
PhD Student,
c/o Dr. R. Sankararamakrishnan,
Bioinformatics and Biomolecular Simulation Lab,
Dept. of BSBE,IIT-Kanpur,
UP-208016:India
email:dennis at iitk.ac.in;dilraj2002 at yahoo.com
mob:09415473973
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