I want to run more than 300 MD, each with a different PDB (more precisely,
variants derived from a same wild type). I need to manually assign the
protonation states using the "-inter" option every time, which is impossible
for more than 300 times.
gmx pdb2gmx -f protein.pdb -o protein_process
Hi,
Echo works just fine - you just need a way to script what input it injects
to the stdin of pdb2gmx. That's logic you need for any solution so is
probably easiest. The expect tool may be another option.
Mark
On Fri., 21 Feb. 2020, 21:41 ZHANG Cheng, <272699...@qq.com> wrote:
> I want to run
Thank you Mark! Sorry could you please explain the details of "stdin" of
"pdb2gmx"? Is there a link for it?
I think "echo" only works for choosing the force field, but not work for the
charge assignment.
e.g. when I use:
echo 15 0 0 0 0 | gmx pdb2gmx -f protein.pdb -o protein_processed.gr
Hi,
On Sat, 22 Feb 2020 at 14:07, ZHANG Cheng <272699...@qq.com> wrote:
> Thank you Mark! Sorry could you please explain the details of "stdin" of
> "pdb2gmx"? Is there a link for it?
>
The stdin stream is a fundamental concept in how unix terminals work. The
echo tool fills that stream for pdb2
Thank you Mark!
I have tried version 2019.3 as well.
Again, the manual input works all fine
https://github.com/lanselibai/gromacs-20200223/blob/master/manually_type
but the command using "echo" still had the same problem
https://github.com/lanselibai/gromacs-20200223/blob/master/echo
I also
