[gmx-users] Gromacs with InflateGro

[Tsjerk Wassenaar]

Hi Anthony,

I'm currently working on an alternative program to put things in an AA
membrane. If you want, you can send me the protein (off-list) and I can
give it a try.

Cheers,

Tsjerk

On Sun, Mar 8, 2015 at 6:03 PM, Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> Hi all,
>
> I'm really struggling to get InflateGro to work in a dimer + lipid (no
> water or ions) system. The fault seems to happen when the regular
> expression to break the .gro entry reads in an entry from C 9999 to C10000.
> I managed to generalise the regex further and now using substr to
> explicitly pull out the entries I want. Unfortunately I'm a little confused
> as to the purpose of a variable called 'now'.  Has anyone got a bullet
> proof copy of the code working with +9999 atoms as I've had enough going
> through this file.
>
> I also tried InflateGro2, which passes the first two iterations but then
> dies after the second. It can't find tmp_out.gro, as the previous entry
> hadn't successfully passed grompp due to a difference in atom count between
> .gro and .top.
>
>
> Thanks
> Anthony
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-- 
Tsjerk A. Wassenaar, Ph.D.