[gmx-users] making topology file for infinite crystal
Vishal Agarwal
vishal.iitian at gmail.com
Sun Feb 7 22:13:28 CET 2010
Dear Justin,
Thanks for replying. I really appreciate this.
Thanks,
Vishal
On Sun, Feb 7, 2010 at 3:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>
>> ========================================
>> -- 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> 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
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