[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
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:
> 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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Catarina A. Carvalheda
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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