[gmx-users] charmm gui pdb to gro.

[Sahil Lall]

Hey, 

You could use pdb2gmx on the CHARMM-GUI ".pdb" output. The -ignh flag
allows for ignoring preexisting hydrogen atoms if that's really
required. 

Cheers, 

Sahil

On 2020-01-14 12:23, Yogesh Sharma wrote:

> Greetings,
> hey, I want to convert the charmm gui generated pdb (membrane + protein) to
> gromacs readable file.  charmm generated lipids contain hydrogen atoms and
> naming differences. I tried doing it manually but couldnt succeed. Is there
> any script available for atom renaming and reordering?
> 
> I also tried manual packing of POPC molecules from this site (
> http://wcm.ucalgary.ca/tieleman/downloads) around oriented protein
> extracted from charmm gui bilayer builder but simulation was not successful
> probably i couldnot pack it properly (didn't get any error though. packing
> was performed using inflategro with shrinking to a final area of 74A^2).
> Charmm gui generated output is working fine with water but I want to
> perform complete simulation in 54A7 ff due to ligand parameters
> availability. hence, i have to convert charmm gui generated output to gro
> format. Is there any way around?