[gmx-users] making topology file for infinite crystal
Justin A. Lemkul
jalemkul at vt.edu
Sun Feb 7 19:18:58 CET 2010
Vishal Agarwal wrote:
> Dear Justin,
>
> Thanks for replying.
>
> pdb2gmx -f cellulose.gro
>
>
> So then your "cellulose.gro" contains all the atoms of GLCA
> monomers, named exactly as the force field expects them? Have you
> checked against the .rtp entry? What force field are you using?
>
> ;;
>
> Should they be exactly in the same order as the rtp entry ? The atom
> type I specified is definitely according to the standard convention of
> rtp entry. I am using G45a3 as the force field.
>
Not to my knowledge. As long as all of the expected atoms are there, you
shouldn't have a problem.
>
> I am getting the following error while using pdbgmx.
>
> "Fatal Error:
> Atom -O not found in residue 2 while adding improper"
>
> Atom type "O" is actually not part of the GLCA residue. Only
> atom type OA is part of GLCA residue.
>
>
> pdb2gmx is complaining about an atom, not an atom type. Somewhere
> in the .rtp file (probably within the [impropers] section, there
> should be a line specifying an atom named O that belongs to the
> preceding residue (hence the minus sign). None of my .rtp files are
> like this. Did you create a custom .rtp entry?
>
> ;;
> No I didnt create a custom rtp entry.
>
>
> Do I need to modify the rtp entry to suit my system or does this
> error corresponds to something else ?
>
>
> That will depend upon the answers to the above questions. If you
> created the .rtp entry, then you'll have to fix the problem of
> naming mismatch. If you're using the standard .rtp entry for the
> force field, then it's easier to modify your coordinate file to
> match the naming expected by the force field.
>
> ;;
> The problem I am having is where to modify my coordinate file. The
> residue doesnot contain a atom type 'O'.
>
> Another curious question I have is suppose if I have another system
> where the a monomer uint say GLCA (specified in rtp) is connected by a
> bridging atom say Carbon. Do I need to create a new rtp entry for pdbgmx
> to work or is there a work around by specifying that carbon as a
> separate residue ?
>
The problem comes from this line in ffG45a3.rtp:
[ impropers ]
; ai aj ak al gromos type
C1 O5 -O C2 gi_2
Clearly the force field is expecting to assign an improper around carbon C1
using an "O" atom in a previous unit as a reference. I think this may be a typo
in the file. The ffG53a6.rtp file has this line for the same improper:
C1 O5 O1 C2 gi_2
I think this is what was intended. I do not know why the anomeric carbon would
be using a previous residue as a reference for assigning an improper. Perhaps
this is a bug. Make a local copy of ffG45a3.rtp and fix the line to make it
look like the ffG53a6.rtp entry. Please report back if this works; it may need
to be fixed for a future release.
-Justin
>
> Again thanks for replying.
>
> Best,
> Vishal
>
> -Justin
>
> Your help is appreciated.
> Thanks,
> Vishal
>
> On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Vishal Agarwal wrote:
>
> Dear Mark,
>
> What I meant over here is the missing oxygen (-O) which
> pdbgmx
> complains about is not a part of .rtp entry. There is no such
> type of oxygen specified in any of the .atp entry of the
> forcefield I am using.
>
>
> The "-O" is not an atom type, it indicates an oxygen atom of a
> previous residue. It is still not clear what it is you're
> doing or
> what the actual problem is. If you want a resolution, you'll
> have to
> do as Mark asked and post your command line and the actual error
> message. Remember, you're asking for free help - you have to
> make
> it easy for us to help you.
>
> -Justin
>
> Vishal
>
>
> On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>>> wrote:
>
> On 07/02/10 14:52, Vishal Agarwal wrote:
>
> Dear All,
>
> Can anyone help me how can I go about preparing
> the topology
> file for an
> infinite crystal of cellulose. I have prepared the
> .gro
> file for
> 5X5X5
> unit cells of cellulose II using GROMACS utility and
> intend to apply
> periodic BC on it. It has a glucose molecule as
> building
> block
> (GCLA).
> When I try running pdbgmx, I get an error for
> extra hydrogens
> (which is
> not there in itp file but is actually there in the
> original
> structure
> which I am using) and missing oxygen (-O).
>
>
> People who might help aren't at all interested in your
> description
> of the error message. If the contents of your head
> were reliable,
> you wouldn't have seen the error in the first place,
> or would
> have
> solved the issue already. :-) Copy and paste your command
> line, and
> what seems to be the relevant part of the error.
>
> To use pdb2gmx, you need .rtp file entries that
> correspond to
> your
> monomers. If not, you will not be able to use pdb2gmx
> to generate
> your topology files.
>
> Mark
> -- gmx-users mailing list gmx-users at gromacs.org
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>
> -- Regards
>
> ***********************************************
> Vishal Agarwal
> Research Scholar
> University of Massachusetts, Amherst
> ***********************************************
> 'Your only obligation in any lifetime is to be true to
> yourself."
> ---Richard Bach
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
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>
>
> --
> Regards
>
> ***********************************************
> Vishal Agarwal
> Research Scholar
> University of Massachusetts, Amherst
> ***********************************************
> 'Your only obligation in any lifetime is to be true to yourself."
> ---Richard Bach
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
> --
> Regards
>
> ***********************************************
> Vishal Agarwal
> Research Scholar
> University of Massachusetts, Amherst
> ***********************************************
> 'Your only obligation in any lifetime is to be true to yourself."
> ---Richard Bach
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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