On Fri, Apr 12, 2019 at 8:59 AM <[email protected]> wrote:
>
> Hi,
>
> I am having a problem with csg_map. I get the error
> mapping error: molecule 370:CH4N2:C_21 does not exist
> I have attached the folder with the files. Could you possibly explain what is
> the (.gro) format needed in order for votca to process the file.
370:CH4N2:C_21 is wrong, it needs to be 1:CH4N2:C_21 (same for the
other string starting with 370: in ch4n2_mapping.xml, file attached)
The first number in the string is the local residue number inside the
molecule and CH4N2 only has one residue.
You can run "csg_dump --top urea-water_1atm300K_NPT.tpr" to see what
names votca reads for the topology file.
Christoph
>
> Best regards,
> Christianna
>
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Christoph Junghans
Web: http://www.compphys.de
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<cg_molecule>
<name>B</name>
<ident>CH4N2</ident>
<topology>
<cg_beads>
<cg_bead>
<name>B1</name>
<type>B</type>
<mapping>B</mapping>
<beads> 1:CH4N2:C_21 1:CH4N2:O_21 1:CH4N2:N_21 1:CH4N2:N_22 1:CH4N2:H__HB 1:CH4N2:H__HB 1:CH4N2:H__HB 1:CH4N2:H__HB </beads>
</cg_bead>
</cg_beads>
</topology>
<maps>
<map>
<name>B</name>
<weights> 12.010700 15.999400 14.006740 14.006740 1.007940 1.007940 1.007940 1.007940 </weights>
</map>
</maps>
</cg_molecule>
