[gmx-users] Re: ffcharmm27 for HEME

Ramachandran G gtrama at gmail.com
Thu Apr 15 11:11:15 CEST 2010


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
--------------------------------------------------------------------------------------------------

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> 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> 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>
>> 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.
>>
>> 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>> 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>>>
>> >     > *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
>> 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.
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100415/2f802ddc/attachment.html>


More information about the gromacs.org_gmx-users mailing list