[gmx-users] GRO File Merging

Mark Abraham mark.j.abraham at gmail.com
Sat Feb 25 20:59:39 CET 2017


Why are you splitting things up? The whole coordinate file from charmm gui
is the useful thing.


On Sat, 25 Feb 2017 20:21 Sanim Rahman <sanimr at mail.usf.edu> wrote:

> Hi all,
> I have been using gromacs to design a membrane protein system. I used
> CHARMM-GUI to design my membrane and then was able to split my system into
> three parts (protein, lipid, solvent) and convert it into .gro format. I am
> able to individually view each part in VMD all together but when I use:
> *cat protein.gro lipid.gro solvent.gro > system.gro*
> The molecule does not show up in VMD. I properly edit the number of atoms
> and the box coordinates of the system by using -editconf to correct the box
> coordinates. I receive no errors in VMD as well. What should I do to fix
> this?
> Also when combining topology files, I would convert lipid.top and
> solvent.top into .itp files and use the #include statement to combine them
> into my protein.top file? After that, my system should be set correct?
> Thank You,
> Sanim Rahman
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