Dear experts:
I am trying to do the molecular dynamic simulation for protein-surface interaction, the surface (like cellulose or PET) is a film-like or crystalline material with large surface area, I had tried different software but did not succeed...
NAMD : It is the software now I am trying, from the tutorial file I did learn how to run equilibrium and energy minimization for solvated protein system, but I am not sure if it support the function that can combine the protein with non-protein macromolecular surface and analyze their binding affinity and interaction energy.
I tried GROMACS and Protpos (GROMACS-based) before, which the topology file (itp) for non-protein molecule should be generated by external tools, but the tools I found only support molecule with atoms less than 1000, and I don't know how to create large surface macromolecular's itp file by myself.
Could you please give me some suggestions about the applicable software to run for this purpose, explain or give me a link of tutorial about how to run it ?
Thanks for your patience.
The files appended are related thesis I have been accessed to, they have briefly mentioned the methodology using CHARMM or NAMD for this purpose.
If I understand your question correctly in that you are running protein -- material interaction chemistry consider looking at DL-POLY. I only have limited experience with it, however, I shared an office with several theoretical material chemists and it seemed to be the go-to software:
http://www.ccp5.ac.uk/DL_POLY_CLASSIC
One other suggestion would be Material Studio, but it's very expensive.
Thank you Anthony Nash , I have tried to installed DL_POLY_Classic, but there was makefile error , I have copied makefile to "source" subdirectory following the manual's instruction and tried to run it on terminal,
when I typed "make gfortran"
it gave: make: *** No rule to make target 'gfortran'. Stop.
then I typed: make -f MakePAR
It gave: Error - please specify a target machine!
Permissible targets for this Makefile are:
debug (parallel)
dlpoly (parallel)
I typed "make dlpoly" , but there was still error message :
it gave: f77 dlpoly.f -o dlpoly
dlpoly.f:30:9:
use angles_module
1
Fatal Error: Can't open module file ‘angles_module.mod’ for reading at (1): No such file or directory
compilation terminated.
: recipe for target 'dlpoly' failed
make: *** [dlpoly] Error 1
Do you know how to fix it ?
I appreciate a lot, thank you!
Anthony Nash this is the manual for you to refer to understand my question about installation. The instruction I followed is on page 83 from session 3.2, I wonder if you have experience on installing similar program, could you please give some suggestions? thank you a lot!
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running