[gmx-users] position restraint on crystal water
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 14 10:27:32 CEST 2005
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 Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list