CCL: MD Simulation by gromacs



Hi Maria,
 You need to first confirm the protonation state of HIS residues for your
 system. Then look at the residues in the rtp file and rename the HIS
 residues (in you pdb/gro) file and then run the pdb2gmx command.
 It is better you send the gromacs related messages to the gromacs mailing
 list. You might end up help from others also.
 Chandan
 On Fri, Oct 28, 2016 at 6:56 AM, Maria khan mariabiochemist1]-[gmail.com <
 owner-chemistry : ccl.net> wrote:
 >
 > Sent to CCL by: "Maria  khan" [mariabiochemist1###gmail.com]
 > Hello dear  gromacs users..
 > I am running simulation for protein ligand complex that are Glutamate
 > racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in
 > residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting
 > atoms.For a hydrogen, this can be a different protonation state, or it
 > might have had a different number in the PDB file and was rebuilt(it might
 > for instance have been H3, and we only expected H1 & H2).Note that
 > hydrogens might have been added to the entry for the N-terminus.Remove
 > this hydrogen or choose a different protonation state to solve it.Option
 > -ignh will ignore all hydrogens in the input."for making pdb2gmx and
 it
 > doesnt form topology file.
 > where am i doing wrong.
 > kindly help me out.
 > Regards and thanks
 >
 >
 >
 > -= This is automatically added to each message by the mailing script =->
 >
 >
 --
 Chandan Kumar Choudhury
 Post Doctoral Fellow
 Clemson University
 South Carolina
 USA
 *"All work and no play makes Jack a dull boy...”*