[gmx-users] position restraint on crystal water
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 14 15:49:29 CEST 2005
On Thu, 2005-07-14 at 19:00 +0530, Dilraj Lama wrote:
> 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"??????????
By making only the restrained ones SOLA
>
> 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
> gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
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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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> >
> >
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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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> gmx-users at gromacs.org
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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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