normal Addition of ions in martini v2.2

  • anuvc84
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11 years 1 month ago #1382 by anuvc84
Addition of ions in martini v2.2 was created by anuvc84
Dear users,
I am trying to do a coarse grained simulation of an octamer using martini_v2.2 in gromacs 4.5.3.
While preparing the system it showed a net charge of 64. So I added Na+ ions using genion with martini_v2.0_ions.itp file. Further, grompp was run including this itp file. but it showed an error -

"Fatal error:
Topology include file "martini_v2.0.itp" not found"

So do I need to use the older version of martini force field (v2.0) or is there a way to overcome this error with the new force field (v 2.2) itself?

Thank you
Regards
Anu

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11 years 1 month ago #1383 by djurre
Replied by djurre on topic Addition of ions in martini v2.2
Martini 2.2 for proteins is in principle compatible with the 2.0 force field for ions and other molecules (such as lipids).

However you don't have to include "martini_v2.0.itp", only include "martini_v2.0_ions.itp".

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11 years 1 month ago #1384 by anuvc84
Replied by anuvc84 on topic Addition of ions in martini v2.2
Thank you for the reply. I have included the line

#include "martini_v2.0_ions.itp"
in the topology file along with martini_v2.2.itp. even then it showed the following error

"Fatal error:
Topology include file "martini_v2.0.itp" not found"

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11 years 1 month ago #1385 by djurre
Replied by djurre on topic Addition of ions in martini v2.2
There must be an include statement referring to "martini_v2.0.itp" somewhere in your top or itp files.

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11 years 1 month ago #1386 by anuvc84
Replied by anuvc84 on topic Addition of ions in martini v2.2
Thank You.I found a statement reffering to martini_v2.0 in the topology file.Now it ran fine
with regards
Anu

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