[gmx-users] Re: ffcharmm27 for HEME
gtrama at gmail.com
Thu Apr 15 11:11:15 CEST 2010
Using the latest git i could able to work on my oxy-hemoglobin
system with new gromacs version 4.0.5 successfully. But since my new gromacs
version was not installed in parallel i tried using older version of gromacs
3.3.1 which was installed in parrallel. While doing grompp to get the *.tpr
file, i am getting the below error.
Program grompp, VERSION 3.3.1
Source code file: topdirs.c, line: 103
Invalid dihedral type 9
I am planning to install the newer gromacs version also in parallel but in
the mean time i also wanted to rectify the above error, if i can. Thank
On Thu, Mar 18, 2010 at 3:02 AM, Pär Bjelkmar <bjelkmar at cbr.su.se> wrote:
> I have now added the charmm files to git head and the protein and lipid
> parts should work at least. Simply check out the latest git and the charmm
> parameters should show up in pdb2gmx.
> 11 mar 2010 kl. 03.04 skrev Ramachandran G:
> Hello Bjelkumar,
> Thanks for your reply. I will wait until you add the new force
> field to the git.
> On Tue, Mar 2, 2010 at 12:47 AM, Pär Bjelkmar <bjelkmar at cbr.su.se> wrote:
>> I have that on my schedule for next week. That is to add the new force
>> field format to the git source code tree. Until then you could use the old
>> format if you checkout a previous version of the source code. I guess you
>> know about git otherwise there's some info here
>> So start by getting a copy of the latest _developing_ version (git head)
>> of gromacs source code:
>> $ git clone git at git.gromacs.org:gromacs.git
>> The force field files were update in end of January to you could checkout
>> a version from Jan 27 by:
>> $ git checkout d80138d720fd41a5005238adecd5bfd5400e524c
>> then compile. Now it should work if you got the HEME parameters from
>> Michel. Alternatively you wait until end of next week when I think I have
>> had time to add the new force field format to the git head.
>> Good luck!
>> 1 mar 2010 kl. 21.21 skrev Ramachandran G:
>> 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
>> 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.
>> ---------- Forwarded message ----------
>> From: Michel Cuendet <michel.cuendet at isb-sib.ch>
>> Date: Fri, Feb 26, 2010 at 1:03 PM
>> Subject: Re: ffcharmm27 for HEME
>> To: Ramachandran G <gtrama at gmail.com>
>> 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.
>> 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
>> > <michel.cuendet at isb-sib.ch <mailto:michel.cuendet at isb-sib.ch>> 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
>> > parameters seem to be inconsistent. For example, the FE-OM-OM angle
>> > 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
>> > corrected this and guessed a couple of missing parameters for our
>> > 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
>> > the HEME we can distribute the dihedral over NA, NB, NC, and ND. So
>> > divide the original force constant (0.2092) by four. This should
>> > 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 <gtrama at gmail.com
>> > <mailto:gtrama at gmail.com> <mailto:gtrama at gmail.com
>> > <mailto:gtrama at gmail.com>>>
>> > > *Datum: *22 februari 2010 23.56.42 CET
>> > > *Till: *bjelkmar at cbr.su.se <mailto:bjelkmar at cbr.su.se>
>> > <mailto:bjelkmar at cbr.su.se <mailto:bjelkmar at cbr.su.se>>
>> > > *Ämne: **ffcharmm*
>> > >
>> > > Hi Pär Bjelkmar,
>> > > Thank you for the charmm force field patches for gromacs. It
>> > > 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.
> Postdoctoral Research Scholar,
> Department of Chemistry,
> University of Nevada, Reno.
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