Dear Pär Bjelkmar,
After getting help from Michel Cuendet still i am
facing problem and i
understood that in groamcs latest version 4.0.x problems may
come due to CMAP.
He suggested me to seek your help. Could you help me to get
new toplogy
format charmm files which can adapt the HEME sections to that.
Thank you.
Rama
---------- Forwarded message ----------
From: *Michel Cuendet* <[email protected]
<mailto:[email protected]>>
Date: Fri, Feb 26, 2010 at 1:03 PM
Subject: Re: ffcharmm27 for HEME
To: Ramachandran G <[email protected] <mailto:[email protected]>>
Dear Mr. Ramachandran,
This means you are using grompp from the distribution version
4.0.x.
This version of gromacs does not know about the CMAP
forcefield term.
You have two options :
1) Deactivate CMAP. This would be equivalent to using the
charmm22 ff
instead of the charmm27, which many people consider fine. To
do this,
edit the file ffcharmm27.rtp and delete all [cmap] sections. This
_should_ work.
2) Download the git development version, which knows how to
handle CMAP.
I know they have been changing topology formats in the latest
versions,
but I hope it is still able to read the old topologies.
Otherwise, you
will have to ask Par Bjelkmar for the charmm files in the new
topology
format, and adapt the HEME sections to that.
Sorry it is a bit messy at the moment. But everything should
become part
of the gormacs4.1 distribution.
Bye,
Michel
Ramachandran G wrote:
> Dear Mr. Michel,
> Thank you very much for you help and time.
> Although i could able to do pdb2gmx and get the *.top file
still, i
> have problem in getting the 'tpr' file using grompp. This
is due the
> 'cmap'
>
> I would try to fix the problem myself but still if the
problem persist
> then i will get back to you. Thank you again.
>
> regards,
> Rama
>
> On Thu, Feb 25, 2010 at 8:59 AM, Michel Cuendet
> <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
>
>
> Dear Mr. Ramachandran,
>
> Attached is a tar file containing the ffcharmm27
forcefield files
> modified for the HEME and an optional CO ligand.
>
> Note that I also wanted to add the O2 ligand, but the
original charmm
> parameters seem to be inconsistent. For example, the
FE-OM-OM angle is
> 180deg, which is wrong. And there is no angle defined
for NH2-FE-OM,
> while a strong angle is required to keep the ligands
axial. So we have
> corrected this and guessed a couple of missing
parameters for our own
> use. But I do not include them to the official ffcharmm27
> distribution,
> which should stay as close as possible to the original
charmm
> force field.
>
> There is a subtlety with the histidine binding to HEME.
The Charmm
> patch
> PHEM defines a dihedral term only with NA and not with
NB,NC, or ND.
> ; 1CD2 1NE2 2FE 2NA (1 = HSD, 2 = HEME)
> In gromacs we cannot differentiate between NA, NB, NC,
and ND of the
> heme (and special values cannot be attributed in the
rtp file for
> dihedrals involving atoms from other residues). Given
the symmetry of
> the HEME we can distribute the dihedral over NA, NB,
NC, and ND. So we
> divide the original force constant (0.2092) by four.
This should give
> pretty much the same behavior in practice.
>
> In order to treat the HEME with pdb2gmx, you have to
(assuming the
> HEME
> is covalently bound to an histidine in chain A):
>
> 1) Attribute HEME to chain A (Covalent bonds only
within one chain)
>
> 2) Move HEME to end of chain A (all atoms of one chain
have to be
> consecutive for gromacs)
>
> See the attached pdb file as an example.
>
> I hope it will work. Do not hesitate to contact me if
you have any
> additional questions,
>
> Best regards,
> Michel
>
>
>
> > *Från: *Ramachandran G <[email protected]
<mailto:[email protected]>
> <mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
> <mailto:[email protected] <mailto:[email protected]>>>>
> > *Datum: *22 februari 2010 23.56.42 CET
> > *Till: *[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
> <mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
> > *Ämne: **ffcharmm*
> >
> > Hi Pär Bjelkmar,
> > Thank you for the charmm force field patches for
gromacs. It is
> > very much useful for me. However presently i am facing a
problem
> since
> > these force fields do not have 'HEME' group in it. I
tried to
> add it
> > manually but unsuccessful. Could you help me in adding
the HEME
> group
> > to the ffcharmm patches. Your help would be highly
appreciated.
> >
> >
> > Ramachandran. G
> > --
> > Postdoctoral Research Scholar,
> > Department of Chemistry,
> > University of Nevada, Reno.
>
>
>
>
> --
> Postdoctoral Research Scholar,
> Department of Chemistry,
> University of Nevada, Reno.
--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
