[gmx-users] making topology file for infinite crystal
Justin A. Lemkul
jalemkul at vt.edu
Sun Feb 7 18:29:32 CET 2010
Vishal Agarwal wrote:
> Dear Justin,
>
> I am trying to make topology file for cellulose II. The monomer unit is
> glucose (residue type GLCA). I do the following:
>
> 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?
>
> 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?
> 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.
-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>> 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>>> 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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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