Re: Using NAMD with NMR structure

From: Pardis Tabaee (
Date: Mon Oct 24 2016 - 16:02:48 CDT

H-NMR is still being used. The problem is probably in the topology file. Sometimes the tutorials are old, so they contain old topology files, but the tutorial files might contain the latest versions, so that could be the reason. I'm sorry I didn't understand what PDF was, I assumed the Hydrogens were important to compare with experimental data, this can be done with NAMD/VMD because the topology file with the Hydrogens is also available (I used it before). Also, I disagree on the coordinate information being different; they are different if you remove them and re-add them, as then you are reassigning positions. Some softwares might also do this, but I think VMD is ok--_000_DB4PR03MB4762519156B00D28E0E7517FDA90DB4PR03MB476eurprd_--

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