[gmx-users] Simulation queries

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Tue Mar 14 13:19:29 CET 2017


1) Make sure that when you replace "HEM" by "HEME" you keep the same
spacing, e.g. `sed 's/HEM /HEME/g' input.pdb > output.pdb` (as opposed to `sed
's/HEM/HEME/g' input.pdb > output.pdb`). If the spacing is not correct it
won't work.

2) No

3) Charmm36 should work just fine if you rename the carbon monoxide and the
heme group properly


On 14 March 2017 at 12:08, Acqualine Lobo <acqualobo02593 at gmail.com> wrote:

> Hi,
> 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
> simulation.
> 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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Catarina A. Carvalheda

PhD Student
Computational Biology Division
University of Dundee
DD1 5EH, Dundee, Scotland, UK

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