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, [EMAIL PROTECTED] 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 [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Or how I learned to stop worrying and love email again _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
