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



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?
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to