Dear VOTCA,
I understood the argument for --map-ignore. The argument is defined in
<name> </name> in xml files. If I would like to ignore the SecondMol and
ThirdMol, I use the following command.
cag_gmxtopol --top topol.tpr --out FirstMol.top --cg
"FirstMol.xml;SecondMol.xml;ThirdMol.xml" --map-ignore "SecondMol;ThirdMol"
Thanks.
Best regards,
Changwoon Jang
On Wednesday, October 14, 2015 at 2:57:46 PM UTC-4, CHANG wrote:
>
> Dear VOTCA users,
>
> I am trying to generate CG topology file using csg_gmxtopol. I have
> three xml files for three types of molecules. I understand that it cannot
> create multiple molecules topologies. Therefore, I need to use --map-ignore
> option. I am not sure what the argument for --map-ignore options is.
>
> Is this xml file or name defined in each xml files?
>
> Can I use a separate run of csg_gmxtopol like?
>
> csg_gmxtopol --top topol.tpr --out FirstMol.top --cg FirstMol.xml
>
> csg_gmxtopol --top topol.tpr --out SecondMol.top --cg SecondMol.xml
>
> csg_gmxtopol --top topol.tpr --out ThirdMol.top --cg ThirdMol.xml
>
> The topol.tpr is the atomistic trajectory for all three molecules.
>
> Thank you very much for your help.
>
>
> Best regards,
> Changwoon Jang,
>
>
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