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

Nelson Cotrim nhcotrim at gmail.com
Thu Jan 17 22:03:39 CET 2008

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:
but that did not solve my problem. I removed all the unnecessary
entries from the hdb file, keeping only the SEP and P data, and then
there was another error in yet another ffG43a1p file (I don't remember
which one right now). I removed all ffG43a1p files and rolled back the
files changed by ffG43a1p to the original ones from Gromacs 3.3.1 and
tried PRODRG.
So far, everything is going smoothly -  I am running the dynamic even
so (it's a small one, takes me just two days of computer time and
there are no other MDs to run), to make sure everything goes right -
the PO3 keeps its tetrahedrical shape, grompp and mdrun runs
smoothly... I just will not be able to use the results because there
is this extra hydrogen atom which I do not know how to remove from the
.gro and .top files.

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