[gmx-users] Simulation queries

Acqualine Lobo acqualobo02593 at gmail.com
Tue Mar 14 13:08:15 CET 2017


I have a couple of questions. I'd be really glad if anybody can help me
with them.

1) The parameters for the Straub Karplus CO model are present in the Charmm
36 forcefield, with residue type CO. In order to use that on my ligand
molecule (CO) I have to change the residue type in my pdb file from CMO to
CO. That works just fine! But since I have a heme group in my pdb file
pdb2gmx throws an error as the Charmm 36 forcefield recognizes the heme
group with residue name HEME and not HEM as it is mentioned in pdb. When I
alter the pdb file and change HEM t0 HEME the pdb file is disrupted. The
entire structure is distorted. What should I do?

2) Can I copy parameters for CO from Charmm and paste them into
Gromos53a5/6? Is that even appropriate?

3) I actually did the above! Because if I use G53a5/6 pdb2gmx throws an
error for CO and if I use Charmm pdb2gmx throws an error for HEME. Using
the above (2) idea I played around with the files and somehow set up a
simulation. The simulation ran well without any errors but the end result
was disastrous (as expected). The  CO molecule splits into C and O during

How can I handle this simulation exercise? Which forcefield should I use? I
want to simulate a Hemoglobin molecule in complex with Carbon Monoxide.

Thanks in advance for any help!

Acqualine Lobo

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