Hi Par and Mark,
Thanks for the suggestions. You may be correct, using gromacs version
4.0.5 Charmm ff didn't worked straight away in my first attempt, but it
works after i made some modification here and there.
Best regards,
Rama
On Thu, Apr 15, 2010 at 2:47 AM, Pär Bjelkmar <[email protected]> wrote:
> Hi,
>
> 15 apr 2010 kl. 11.11 skrev Ramachandran G:
>
> Hello Par:
> Using the latest git i could able to work on my oxy-hemoglobin
> system with new gromacs version 4.0.5 successfully.
>
> CHARMM is not supportd in version 4.0.5, you probably mean the developer
> version?
>
> 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
>
> --------------------------------------------------------------------------------------------------
>
> This is because we have made changes in the source code to allow for the
> CHARMM ff (we added a new dihedral type, see paper, that is causing this
> particular error). So, you have to run with the developer git version.
>
> Regards,
> Pär
>
>
> 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 <[email protected]> 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 <[email protected]> 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 [email protected]: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 <[email protected]>
>>> Date: Fri, Feb 26, 2010 at 1:03 PM
>>> Subject: Re: ffcharmm27 for HEME
>>> To: Ramachandran G <[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]>> 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]>>>
>>> > > *Datum: *22 februari 2010 23.56.42 CET
>>> > > *Till: *[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.
>>>
>>>
>>>
>>
>>
>> --
>> Postdoctoral Research Scholar,
>> Department of Chemistry,
>> University of Nevada, Reno.
>>
>>
>>
>
>
>
>
>
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--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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