thank you for you answer Mr. Rezvan
indeed, I know this site , and my question is: how to merge two topology files of two merged molecules to get a new topology file for the whole system?
thank you
Farhad Zrar Ahmed
You had asked about "combine two charmm force field files" which you could do by simply copy-pasting the content of the files into a new text file but later rephrased it to "merge two topology files". Can you provide more details for what you're trying to do exactly? are referring to NAMD or GROMACS topology files (what are the extension of your files)?
Hi Naeem
I am a new LAMMPS user.
I am working on a project using LAMMPS molecular dynamics simulation, I use a complex system to simulate it, which consists of two molecules. I have a force field (topology file and parameter file with extensions .rtf and .par respectively) for each molecule, now I want to two merge these two force field files? how can I do that?
and you said, you could do this by simply copy-pasting the content of the files into a new text file but later rephrasing it. but how can I rephrase it?
your guide would be appreciated
thank you.
Farhad
Farhad Zrar Ahmed The .par files are parameter files, they contain the forcefield parameters and are plain text files (you can open it notepad-like app), it's order is irrelevant so you could append the content of one to another and it wouldn't cause any issues. I don't use LAMMPS so I don't really know how RTF files are structured but if LAMMPS accepts PSF files (like NAMD), then VMD has a tool called PSF GEN that can convert your PBD+RTF files into a PSF file (which is the topology file).
Dear @Naeem, my project is a molecular dynamics simulation of a complex system which includes two molecules. I got the .RTF and .PAR files for each molecule. now I need to merge the.RTF files to make a new one for the complex system but I dont have enough info. to do that. because this is my first project in this field. furthermore, I know about PSF GEN tool in VMD and used it, but it does not my point because I obtained .PSF files for the comlex system.
very appreciate your guiding Sir.
Regards
Farhad.
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