GROMACS version: 5.1
GROMACS modification: No
Here post your question: Dear All, As per the available commands, I tried to generate a test.top file from VMD psf file/pdb file by using topotools 1.6. By using this test.top file I am trying to generate a test.tpr file for my protein-water system by grompp engine using a sample mdp file. But during this conversion, it is generating one error: ------------------------------------------------------------------ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. ----------------- I searched in google and found one issue that it does not store box length information, that is why no matter what the value of rlist is, it will produce the same error. INfact I also tried with very small value of rlist but still the issue was present. Kindly help me to figure out my queries… (1) If I need to store box information , how is it possible by using VMD topotools or grompp mechanism . (2) Is there any way to avoid the issue, as I need the tpr file only for analysis purpose not for simulation. As I already converted my NAMD dcd file into trr file.
(3) Is there other tools available to convert NAMD psf/pdb/dcd format to tpr format.
Many Many thanks in advance for any kind of help.
regards
Santanu