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? -- 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.