[gmx-users] How to remove H atom from residue in gro file?

Hi gmx users, I am rather new to MD, Linux environment and almost everything related to it. I am a geneticist working on mutations, so please, keep it simple :) This may be trivial and there may be an answer on the list already, but I do not even know how to search for it - the way I tried did not

Re: [gmx-users] How to remove H atom from residue in gro file?

Hi Justin, Thanks for the reply. Yes, I used PRODRG Beta. Thanks for the heads up about the charges. The error I got using ffG43a1 was this: >Fatal error: > wrong format in input file ffG43a1p.hdb on line >2 7 OW which was also described here: http://www.gromacs.org/pipermail/gm

Re: [gmx-users] How to remove H atom from residue in gro file?

Hi Maik, Thanks for the warning and the tip, I have already donwloaded and will read that paper today, it seems to be what I need. I have been working with MD for some 6 months now (I know that's not much), and have had the help of some knowledgeable people, but they are unavailable right now. I ju

Re: [gmx-users] How to remove H atom from residue in gro file?

test it against my ffG43a1p > > files. If it works, I can send you my modifications. I made no changes to > > the > > force field parameters, only the formatting of the files themselves. > > > > -Justin > > > > Quoting Nelson Cotrim <[EMAIL PROT