[gmx-users] Re: ffcharmm27 for HEME
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Apr 15 11:17:18 CEST 2010
On 15/04/2010 7:11 PM, Ramachandran G wrote:
> Hello Par:
> 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
>
> Fatal error:
> Invalid dihedral type 9
> --------------------------------------------------------------------------------------------------
Don't bother with 3.3.1 at all, and don't install 4.0.5 (which has had
many bugs fixed in 4.0.7). Just wait for 4.0.7 to be installed.
Firstly, you have the above compatibility problem. Secondarily, the way
parallel simulations are managed has changed significantly. Search the
GROMACS webpage for discussion here.
Mark
> 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 you.
>
> Rama
>
>
> On Thu, Mar 18, 2010 at 3:02 AM, Pär Bjelkmar <bjelkmar at cbr.su.se
> <mailto:bjelkmar at cbr.su.se>> wrote:
>
> Hi,
>
> 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.
>
> /Pär
>
> 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.
>>
>> regards,
>> rama
>>
>> On Tue, Mar 2, 2010 at 12:47 AM, Pär Bjelkmar <bjelkmar at cbr.su.se
>> <mailto:bjelkmar at cbr.su.se>> wrote:
>>
>> Hello,
>>
>> 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
>> http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage
>>
>> 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!
>> /Pär
>>
>> 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 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* <michel.cuendet at isb-sib.ch
>>> <mailto: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 <mailto: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.
>>>
>>> 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
>>> > <michel.cuendet at isb-sib.ch
>>> <mailto:michel.cuendet at isb-sib.ch>
>>> <mailto: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 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 <gtrama at gmail.com
>>> <mailto:gtrama at gmail.com>
>>> > <mailto:gtrama at gmail.com <mailto:gtrama at gmail.com>>
>>> <mailto: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>>
>>> > <mailto: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 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.
>>
>>
>>
>>
>> --
>> Postdoctoral Research Scholar,
>> Department of Chemistry,
>> University of Nevada, Reno.
>
>
>
>
>
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