What is the difference between .rst, .rst7, .inpcrd, and .mdcrd coordinate files and between .prmtop and .parm7 topology files for Amber 14? Is there any advantage between using a certain file format over another for Amber 14 MD simulations using pmemd, and could it cause an error during the MD simulation if the wrong format is chosen? And what are .mdcrd files for exactly? If I want to view my trajectory after a simulation using the VMD program, what files would I load? I loaded the pdb file with the vmd command, then through the GUI, loaded the .prmtop, then .inpcrd, and then rst files in order. Is this the correct way to view trajectories in VMD?
Visit this, it could be of some help: http://ambermd.org/formats.html
Anwesh Pandey Thank you for your response; I've read that page, but there's a few things that are still unclear to me. From my understanding, I think rst7 and parm7 are new file format types compared to rst, inpcrd, and prmtop? So, is rst7 more appropriate to use as coordinate files for Amber 14 compared to rst and inpcrd files? And similarly, should I be creating my topology files in parm7 format instead of prmtop? I've been trying to view my trajectories in the VMD program but have been having some issues, so I'm not sure if VMD can only open certain types of files and if I should maybe run my MD simulations again but instead use rst7 and parm7 files to make it work?
Also, I was wondering what would be the difference between creating an ncrst file with pmemd/sander instead of an rst or rst7 file? And the difference between creating an .nc file instead of the .mdcrd file? This tutorial uses parm7, rst7, and create nc and ncrst files: http://ambermd.org/tutorials/basic/tutorial0/ , while this tutorial uses prmtop instead of parm7: http://ambermd.org/tutorials/basic/tutorial1/section6.htm , and these tutorials that I started learning Amber with use prmtop and inpcrd files and creates rst and mdcrd files, which is why I followed this example for my simulations: http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
If I'm using Amber 14, which file formats would be best to use?
Sorry, I have a few more questions if anyone can answer these please! According to the Amber manual, .ncrst is an Amber NetCDF Restart format, .rst7 is an Amber Restart format, .nc is an Amber NetCDF format, and .crd is an Amber Trajectory format. Is .crd format the same as .mdcrd format? I'm guessing that .crd/.mdcrd files and .nc files are both trajectory files, so they will contain all the coordinates for every frame throughout the nanosecond simulation, while .rst, rst7, and .ncrst are all restart file formats, so they will only contain the coordinates at the very last frame of the one nanosecond simulation? Can someone please confirm if my understanding is right, or correct me if I'm wrong?
I think I read that .rst7 and .parm7 files are basically the newer file formats for Amber 7 and higher, while .prmtop, .inpcrd, and .rst are for older versions of Amber? So does that mean that using prmtop, inpcrd, and rst files in Amber 14 may lead to inaccurate files generated by sander/pmemd, or does it not matter?
Also, so the difference between the types of trajectory formats is that .mdcrd/.crd files are in ASCII format while .nc is NetCDF format, and basically the only difference is that NetCDF files are faster to write? Does that mean that NetCDF files contain less information than ASCII files, and is VMD/Pymol/UCSF Chimera able to open both ASCII and NetCDf file formats if I wanted to try to view the trajectories?
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