[gmx-users] making topology file for infinite crystal
Justin A. Lemkul
jalemkul at vt.edu
Sun Feb 7 21:58:13 CET 2010
Vishal Agarwal wrote:
> Dear Justin,
>
> Thanks for replying. I guess it should be -O4 from the convention but
> have to look more deeply to figure out that.
> I am noticing a few more things in the ffG45a3.rtp, entries like +N in
> the bonds and angles section. Since there is no atom type N in the
> monomer, are these entries correct or another typo ?
>
Probably another typo, unless glucose suddenly contains nitrogen and no one
notified the scientific community :) I would again suggest modifying the .rtp
entry (in a local copy of the .rtp file), modeled after ffG53a6.rtp, since it
appears to be more reliable. There is no need to alter the [atoms] section, but
it appears some of the bonded directives need some work.
-Justin
> Vishal
>
>
> On Sun, Feb 7, 2010 at 1:18 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>>
> <mailto: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>>>
> <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
> <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
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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>
> <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 <http://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 <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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