On 2/19/15 6:44 AM, Sanchaita Rajkhowa wrote:
Hi, I tried using charmm forcefield to simulate heme but we are getting
warning messages.
WARNING: atom HA is missing in residue HEME 1500 in the pdb file
.
.
.
for all 30 hydrogens.
Later we tried modifying the aminoacids.hdb as:
HEME 3
1 5 HA CA N C CB
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
But the problem still persists. What should be done?? Please help.
In principle, modification of the .hdb is all that you need to do. Did your
additions not fix anything? Or do you just have errors (hopefully fewer) that
persist? The alternative is to upload the structure to the CHARMM-GUI server.
It will process the whole thing and write a coordinate file that is fully
compliant with the CHARMM force field (and provide GROMACS inputs for you).
-Justin
regards,
Sanchaita.
On 19 February 2015 at 09:43, Sanchaita Rajkhowa <srajkhow...@gmail.com>
wrote:
Dear Justin, thank you for the reply. However, I would like to know if
there is any server which can generate parameters for heme to be used in
OPLS-aa? We have already tried in swissparam with failed results. Please
help.
On 18 February 2015 at 21:15, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote:
Dear all, I am trying to simulate a heme containing protein in high
concentration (having hydrogen peroxide). However, I do not know which
forcefield to use. Heme has forcefield in gromos96 but not the forcefield
of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
help.
SwissParam creates CHARMM-compatible parameters, so no, you can't mix
those with GROMOS. CHARMM supports heme, but you have to clean up a lot of
auto-generated angles and dihedrals that don't belong.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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