[gmx-users] (no subject)

i am running protein with ligand complex. i am following the methods given by justin. i am using opls force field. i have converted the protein pdb using pdb2gmx and ligand file using topolgen. after that i have concatenated both in gro and include the lig.itp in topology file. while performing

[gmx-users] il -simulation -reg

Dear users, i am working in the ionic liquids simulation. i am having both anion and cation itp file. i have two query reagrding the simulation. 1. how did the two itp file be combined? 2. how to create the force filed itp files for this molecules? thanks in advances with regards uma -- Gromacs

[gmx-users] Fwd: DSSP- error

Dear gromacs users, i am using gromacs 4.6.2. i tried the secondary structure analysis, using do_dssp. but i got the following error. Fatal error: Failed to execute command: /usr/local/bin/dssp.exe -na ddFyZGQ1 ddTj0ABl /dev/null 2 /dev/null. i am using amd, with cemtos. i downloaded dssp

[gmx-users] dssp

dear sir/madam i am new to gromacs. i am trying to install DSSP,i am having centos. i downloaded the DSSP and pasted it in /usr/local/bin directory while i am running it shows the following error Failed to execute command: /usr/local/bin/dssp.exe -na ddLV8RKo ddvXmynp /dev/null 2 /dev/null

Re: [gmx-users] dssp

Thanks Mr. Erik for your kind reply. yes the file name is dssp.exe only On Thu, Jun 5, 2014 at 3:10 PM, Uma Devi renuma...@gmail.com wrote: dear sir/madam i am new to gromacs. i am trying to install DSSP,i am having centos. i downloaded the DSSP and pasted it in /usr/local/bin directory