From owner-chemistry@ccl.net Fri Oct 28 13:23:00 2016 From: "Chandan Choudhury iitdckc:gmail.com" To: CCL Subject: CCL: MD Simulation by gromacs Message-Id: <-52469-161028115645-16850-F7JWvtaVvBygSrJ0Tcblwg/a\server.ccl.net> X-Original-From: Chandan Choudhury Content-Type: multipart/alternative; boundary=001a1147c8e4bc3b9c053feee628 Date: Fri, 28 Oct 2016 11:56:08 -0400 MIME-Version: 1.0 Sent to CCL by: Chandan Choudhury [iitdckc(a)gmail.com] --001a1147c8e4bc3b9c053feee628 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 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 sortin= g > 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 migh= t > 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 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Chandan Kumar Choudhury Post Doctoral Fellow Clemson University South Carolina USA *"All work and no play makes Jack a dull boy...=E2=80=9D* --001a1147c8e4bc3b9c053feee628 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Maria,
You need to first confirm the proto= nation 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 relate= d messages to the gromacs mailing list. You might end up help from others a= lso.

Chandan=C2=A0

On Fri, Oct 28, 2016 at 6:56 AM, Maria khan mariab= iochemist1]-[gmail.com &= lt;owner-chemi= stry : ccl.net> wrote:

Sent to CCL by: "Maria=C2=A0 khan" [mariabiochemist1###gmail.com]
Hello dear=C2=A0 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<= br> residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting<= br> 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<= br> 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 i= t
doesnt form topology file.
where am i doing wrong.
kindly help me out.
Regards and thanks



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--

Chandan Kumar Choudhury
Post Doctoral= Fellow
Clemson University
South Carolina
USA

"= All work and no play makes Jack a dull boy...=E2=80=9D

<= /div>
--001a1147c8e4bc3b9c053feee628--