Names of molecules to put in xml file during IBI

[Pragati Sharma]

Dear all,

I have some confusion regarding the molecule name to be put in xml as well as topology file during IBI.

In atomistic topology, if the molecule name is 'PI' and for CG, I have taken 'CGPI'.

1. In first map file;  in atomistic section; hexane.xml in hexane tutorial, the names I specified for my molecule are:

<cg_molecule>

 <name>CGPI</name> ; CGPI is the name to be given for CG moleculetype
  <ident>PI</ident> ; PI is moleculetype in atomistic topol.top file;  In hexane tutorial, this is 'Protein'

2. In the second mapp file; hexane_cg.xml  in 'ibi_all' folder of hexane tutorial, my names would be

<cg_molecule>

  <name>CGPI</name> ; for CG
  <ident>PI</ident>; In hexane tutorial, it is 'hexane' , shouldn't it be 'Protein' like in hexane.xml file. Where does this hexane come from. Is it a random choice?

<topology>
    <cg_beads>
      <cg_bead>
        <name>A1</name>
        <type>A</type>
        <mapping>UNITY</mapping>
        <beads>1:RES:A1</beads>; In hexane tutorial, instead of 'RES', there  is hex
      </cg_bead>

I have a question here, where does this 'hex' come from. Should I write any random name here for mapping, like I have written 'RES'. If I put 'PI' or 'CGPI' here instead of RES. error comes that 1:CGPI:A1, bead is not recognised.

3. In the topol.top file in ibi_all folder. should I write the CG name ( CGNRP here) in the moleculetype and molecules directive

 [moleculetype]

CGNRP       3

[ molecules ]
; Compound        #mols
CGNRP          1000

A quick help will be very much appreciated.

Thanks

[Christoph Junghans]

On Wed, Jan 20, 2021 at 11:40 PM Pragati Sharma <praga...@gmail.com> wrote:
>
> Dear all,
>
> I have some confusion regarding the molecule name to be put in xml as well as topology file during IBI.
>
> In atomistic topology, if the molecule name is 'PI' and for CG, I have taken 'CGPI'.
>
> 1. In first map file; in atomistic section; hexane.xml in hexane tutorial, the names I specified for my molecule are:
>
> <cg_molecule>
> <name>CGPI</name> ; CGPI is the name to be given for CG moleculetype
> <ident>PI</ident> ; PI is moleculetype in atomistic topol.top file; In hexane tutorial, this is 'Protein'

This was 'Protein' because the molecule is called like this in topol.top, see:
https://github.com/votca/csg-tutorials/blob/master/hexane/atomistic/topol.top#L5

>
> 2. In the second mapp file; hexane_cg.xml in 'ibi_all' folder of hexane tutorial, my names would be
> <cg_molecule>
> <name>CGPI</name> ; for CG
> <ident>PI</ident>; In hexane tutorial, it is 'hexane' , shouldn't it be 'Protein' like in hexane.xml file. Where does this hexane come from. Is it a random choice?

It depends how you call the molecule in topol.top, it was called
hexane in that case:
https://github.com/votca/csg-tutorials/blob/master/hexane/ibi_all/topol.top#L13

> <topology>
> <cg_beads>
> <cg_bead>
> <name>A1</name>
> <type>A</type>
> <mapping>UNITY</mapping>
> <beads>1:RES:A1</beads>; In hexane tutorial, instead of 'RES', there is hex
> </cg_bead>
>
> I have a question here, where does this 'hex' come from. Should I write any random name here for mapping, like I have written 'RES'. If I put 'PI' or 'CGPI' here instead of RES. error comes that 1:CGPI:A1, bead is not recognised.

In the cg case, we called the residue 'hex', hence that showed here, see:
https://github.com/votca/csg-tutorials/blob/master/hexane/ibi_all/topol.top#L17

For the mapping will, you can just run "csg_dump --top
atomistic_topol.tpr" and look at how the beads are named if you are
unsure.

Same is true for the molecule identifier, just look at the output of
csg_dump to understand what VOTCA reads from the tpr file.

Christoph

>
> 3. In the topol.top file in ibi_all folder. should I write the CG name ( CGNRP here) in the moleculetype and molecules directive
> [moleculetype]
> CGNRP 3
>
> [ molecules ]
> ; Compound #mols
> CGNRP 1000
>
> A quick help will be very much appreciated.
> Thanks
>

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--
Christoph Junghans
Web: http://www.compphys.de