On 10/05/2023 22:38, Raghuvir Pissurlenkar via AMBER wrote:
> Dear Prof. Case
> Link to the tutorial "https://ambermd.org/tutorials/advanced/tutorial22/section1.php”
> The Structure input files I used are "bpti-ff99SBi.prmtopp <https://ambermd.org/tutorials/advanced/tutorial22/files/bpti-ff99SBi.prmtop>, bpti-ff99SBi.inpcrd <https://ambermd.org/tutorials/advanced/tutorial22/files/bpti-ff99SBi.inpcrd>”
> The input file I am referring to is "heat-wat.in <http://heat-wat.in/>” which gets downloaded as "https://ambermd.org/tutorials/advanced/tutorial22/files/md_wat.in”
> [...]
> I am able to successfully execute
> $AMBERHOME/bin/pmemd.cuda -O -i min_wat.in -o min_wat.out -p ../*.prmtop -c ../*.inpcrd -r min_wat.rst -ref ../*.inpcrd
> But when am try running the following command the run fails
> $AMBERHOME/bin/pmemd.cuda -O -i md_wat.in -o md_wat.out -p ../*.prmtop -c ../1_/*.rst -r md_wat.rst -ref ../1_/*.rst
> [...]
> Regards
> Raghuvir
Most likely that is because of the *. In all the commands of the tutorial, replace *.prmtop with bpti-ff99SBi.prmtop, and replace *.rst with the actual name of the restart file generated in the
previous step. For example, in the second command, use min_wat.rst; then in the next command, use md_wat.rst, etc. Also, the example commands expect these files each in a directory of its own, so you
either have to move them there by hand, or change the command accordingly.
Also, it is a good idea to read the manual, where the syntax of the all the tools is explained.
Cheers,
Charo
--
Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
Coventry CV1 5FB
UK
https://charodelgenio.weebly.com
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Received on Wed May 10 2023 - 23:30:02 PDT
