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
--
Join us on Slack: https://join.slack.com/t/votca/signup
---
You received this message because you are subscribed to the Google Groups
"votca" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To view this discussion on the web visit
https://groups.google.com/d/msgid/votca/CAMpF9Q2-YfSFE41EN4DQF%2Bm1g6nexzmUCtTdjeLGAUvk9Vm0YQ%40mail.gmail.com.
