Re: [gmx-users] Partial charge distribution for metal ligating atoms

raja wrote: Hi gmxions, There are many references, say that Zn2+ partial charge should be reduced to ~0.7 rather than the force field default value of 2. In line with that there are many values published for distributed charge in its surrounding ligand atoms in compensation for loss of positive c

Re: [gmx-users] Fatal error:;Too many LINCS warnings (10716)

E.Elavazhagan wrote: Hai folks, Thanks for ur previous valuable suggestions. On executing the mdrun command we get the following error. mdrun -v -s pr -e pr -o pr -c after_pr -nice +5 -g pr_log --- Program mdrun, VERSION 3.3.1 Source code fil

[gmx-users] Partial charge distribution for metal ligating atoms

Hi gmxions, There are many references, say that Zn2+ partial charge should be reduced to ~0.7 rather than the force field default value of 2. In line with that there are many values published for distributed charge in its surrounding ligand atoms in compensation for loss of positive charge of Zn. N

[gmx-users] Fatal error:;Too many LINCS warnings (10716)

Hai folks, Thanks for ur previous valuable suggestions. On executing the mdrun command we get the following error. mdrun -v -s pr -e pr -o pr -c after_pr -nice +5 -g pr_log --- Program mdrun, VERSION 3.3.1 Source code file: clincs.c, line: 5

Re: [gmx-users] How to assigne different initial velocities to different groups?

陳 星男 wrote: > Hi : > I want to assign the initial velocities at 300K for one group, 10K for > the rest. Could it be done by set "gen_vel = 300 10" in .mdp file? > Thanks No. Your best chance without doing any code hacking is to equilibrate with those groups coupled to different temperatures,

[gmx-users] How to assigne different initial velocities to different groups?

Hi : I want to assign the initial velocities at 300K for one group, 10K for the rest. Could it be done by set "gen_vel = 300 10" in .mdp file? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Script for coverting ITP and gro file to Autodock pdbqs

raja wrote: Hi gmxions, I want to use charge information contained in itp file produced in gromacs for docking purpose (Autodock). Kindly share a script if anyone written to convert information content from gromacs protein's itp (for charge) and gro (coordinate) information to autodock pdbqs or p

Re: [gmx-users] charges in polymer

Dmitriy Golubobsky wrote: Dear Guru, i need an advice. i create 3 resudues for my polymer. ( begin-monomer, middle-monomer, end-monomer) optimize geometry and charges in gaussin 6-31G. formalize topology for OPLS force-field. but, i've got a question have i to do RESP of the charges of my monom

[gmx-users] Re: Problem in AFM pulling, direction and output?

Dear all: Thank you very much,Emily Walton! Thank for all here! My pull.ppa file is shown in the following: verbose = no runtype = afm ngroups = 1 group_1 = Lig reference_group = Protein reftype = com pulldim = Y Y Y ; afm_rate1

[gmx-users] number of solvent molecule

Hi gmxusers, I am a new user of gromacs. I completed a MD run of my protein in a solvent box. Now I want to calculate the number of solvent molecules (molecules/cc) present arround a shell of 0.6nm from my protein (or sidechains). Please help me. Thanks in advance Chiradip Chatterjee Chiradip Chat

[gmx-users] Fw: Gromacs-3.3.1 configure error in Linux with lam mpi

Hi Zhang,Please have a look at you config.log and see the error message(s) therein. Most likely, it's a problem with the access to the shared libraries: libgm.soI am forwarding your message to the list so that you can get further help.best,pb-- Forwarded message --From: qfzhang <[EM

[gmx-users] Script for coverting ITP and gro file to Autodock pdbqs

Hi gmxions, I want to use charge information contained in itp file produced in gromacs for docking purpose (Autodock). Kindly share a script if anyone written to convert information content from gromacs protein's itp (for charge) and gro (coordinate) information to autodock pdbqs or pdbq formated o

[gmx-users] Official charmm support

Dear gromacs users, I'm a new PhD student in Erik Lindahl's group and we are currently working on an "official" implementation of the charmm ff in gromacs which also supports CMAP. There's still some more work needed on the CMAP part but we intend to have a (thoroughly) tested version of the prote

[gmx-users] charges in polymer

Dear Guru, i need an advice. i create 3 resudues for my polymer. ( begin-monomer, middle-monomer, end-monomer) optimize geometry and charges in gaussin 6-31G. formalize topology for OPLS force-field. but, i've got a question have i to do RESP of the charges of my monomers according to ff or not? i