[gmx-users] Including water in for restraining

[raja]

Hi Chris,
Thanks for your effort to write me the detailed reply. In fact I tried
to put harmonic restraint to one water molecule bound on Zn2+ within the
active site of protein of my interest. The crystal structure reports
four ligating atoms with Zn2+, in addition to H20; other three are from
two NE2 atoms from HIS and one SD atom from CYS residues. I wanted to
use bonded harmonic potential restraints for all those atoms so I edited
original “protein_ion_A.itp” file, which contains information for
protein and Zn alone.
 
This is the addition at the end of [bonds] section of protein_ion_A.itp
done by me
-----------------------------------
 1747  2900     6  0.206 1673.6
 2442  2900      6  0.248 1673.6
 2505  2900     6  0.250 1673.6
 2905  2900     6  0.251 1673.6
------------------------------------

Where 1747 , 2442, 2505 are atom numbers of NE2 of 2 HIS and SD of Cys,
2900 is the Zn2+ but 2905 is the water-oxygen atom number which I
referred from protein.gro file  and usage of this, is causing me the
error which I posted in my previous mail regarding this topic. I think
the water is to be placed in the same file for this to work...but how to
do that is not clear to me.. since no separate itp file is not created
for water topology within the folder, so I can merge them with
protein_A_ion.itp file by any of the scripts available as per some
pervious postings
(http://www.gromacs.org/pipermail/gmx-users/2005-October/017359.html )


Hope you can help me better now.

Thanks in advance!
B.Nataraj











On Sat, 11 Nov 2006 01:17:43 -0500, chris.neale at utoronto.ca said:
> > While I am using harmonic restraint for water and Zn, I am unable to do
> > so since the chain A "itp" file does not contain water, It shows error
> > as follow -------------------------------------------------------
> > Program grompp, VERSION 3.3.1
> > Source code file: toppush.c, line: 1108
> > Fatal error:
> > [ file "Protein_ion_A.itp", line 5847 ]:
> >             Atom index (2905) in bonds out of bounds (1-2900)
> > -------------------------------------------------------
> > How to restraint molecule which is present in out of this itp file ?
> 
> Look at the end of your topol.top file. Does it contain any mention of  
> water, ions, or zinc? If not, then it should contain lines like this  
> (although the exact nature will depend on the water model):
> 
> ; Include water topology
> #include "tip3p.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
> 
> Then in your .mdp file include the line
> define = -DPOSRES_WATER
> to position restrain the water.
> 
> For Zn it will look like this
> ; Include generic topology for ions
> #include "ions.itp"
> 
> This won't work for position restraints. Therefore first look at  
> ions.itp. Notice that there are multiple entries for each ion that  
> correspond to the forcefield that you are using. For this example,  
> let's say that you are using opls-aa:
> 
> You would then remove 2 the lines:
> ; Include generic topology for ions
> #include "ions.itp"
> 
> and add the following lines in their place:
> ; Taken from OPLS-AA from gromacs-3.3.1
> [ moleculetype ]
> ; molname       nrexcl
> ZN2+            1
> [ atoms ]
> ; id    at type res nr  residu name     at name  cg nr  charge   mass
> 1       ZN2+    1       ZN2+            ZN       1      2        65.37000
> #ifdef POSRES_ZN
> ; Position restraint for ZN2+
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
> 
> Then in your .mdp file include the line
> define = -DPOSRES_ZN
> to position restrain the zinc.
> 
> To constrain both, do
> define = -DPOSRES_WATER -DPOSRES_ZN
> 
> Further, whatever file you are using that contains the position  
> restraints for your protein... remove any lines that reference water  
> or zinc.
> 
> If you need further help, please specify exactly what you have done so  
> far, where you got your files, and what the files look like.
> 
> Chris.
> 
> 
> 
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
  raja
  raja_28 at fastmail.us

-- 
http://www.fastmail.fm - Or how I learned to stop worrying and
                          love email again