Re: TopoTools for tpr file

From: Daniel Aguayo (bioquimico_at_gmail.com)
Date: Fri Sep 09 2011 - 10:46:33 CDT

Dear Hasan

Here is part of my script that can help you
You need a mdp file for gromacs ..

set editconf "/Users/daniel/bin/gromacs/bin/editconf"
set grompp "/Users/daniel/bin/gromacs/bin/grompp"
set make_ndx "/Users/daniel/bin/gromacs/bin/make_ndx"

# FILES INPUTS
set filename ionized

# Write Gromacs Compatible Top and tpr
# WARNING JUST FOR ANALISIS !!!!!!!
if { [file exists ${filename}.top] == 0} {
package require topotools
topo writegmxtop ${filename}.top
}
## Gromacs Files
# gro & tpr

if { [file exists ${filename}.gro] == 0 || [file exists ${filename}.tpr] == 0} {
            catch {exec $editconf -f ${filename}.pdb -o ${filename}.gro -nopbc}
            catch {exec $grompp -f m.mdp -c ${filename}.gro -maxwarn 10 -p ${filename}.top -o ${filename}.tpr }
    }
                    

    
On Sep 9, 2011, at 11:01 AM, Hasan haska wrote:

> Dear NAMD users,
>
> I loaded my .psf and then loaded .pdb file into psf in VMD then used the command “ topo writegmxtop myfile.top” in tk console. I finally generated a .top file successfully. But how can I generate a gromacs tpr file using this .top file ? Can you please give me the information about generating tpr file ?
>
> Thanks a lot for your help.
>
>

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