When I use PRODRG to get pdb file I get errors in GROMACS. It says that the Residue 'DRG' not found in residue topology database. How should I do that manually? Does anyone have the files for a triglyceride?
If you use PRODRG, you already have a topology, so there is no need to run pdb2gmx on that molecule. But if you use PRODRG, be prepared to fix the flawed topology.
Your request for "a triglyceride" is far too generic. Triglycerides are structurally diverse.
Hi Justin, thanks for you fast reply. the TOPOLOGY file that I got from Prodrg for using gromacs was ".itp" file. how can I change it to ".top" ? and how can I fixed the topology? indeed I want to use your tutorial "buiding Biphasic system" for triglyceride (any kind for now :) ) water system....
The differences between .itp and .top are superficial, but an .itp file corresponds to a single molecule type, while a .top describes an entire system. You should use the .itp file in an #include statement. There are numerous lipid parameter sets available; you should do a bit of searching to find a suitable one. Fixing the PRODRG topology should be fairly trivial in this case, as most of what you have are uncharged carbons.
THANKS :). I try to do that and I probably come back with more qauestions :)
Have you solved your problem Negar?. I'm trying to simulate a biphasic system for triglycerid, but I can´t get the .gro/.top files..
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