[gmx-users] making topology file for infinite crystal
Vishal Agarwal
vishal.iitian at gmail.com
Sun Feb 7 19:02:09 CET 2010
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.
>> 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 ?
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>> 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
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto: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> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>> Please don't post (un)subscribe requests to the list. Use the www
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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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
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