[gmx-users] position restraint on crystal water

Dilraj Lama dennis at iitk.ac.in
Thu Jul 14 08:11:48 CEST 2005

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


; Include Position restraint file for selected residues of protein
#include "posre_select_protein.itp"

; Include crystal water topology
#include "hoh.itp"

; Include Position restraint file for crystal water
#include "posre_cryst_water.itp"

; 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
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


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
>> 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
>> >>
>> >>                   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
>> 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,
email:dennis at iitk.ac.in;dilraj2002 at yahoo.com
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