On Wed, Jul 7, 2021 at 13:23 Rishabh Guha <[email protected]> wrote: > Hello, > > I have an atomistic system consisting of 250 alanine and 250 valine > molecules. I am trying to use cg_map using the pdb file and the LAMMPS > output trajectory, but I am getting an error:- > cannot find: <1:VAL:CA> in VAL > an error occurred: > mapping error: molecule 1:VAL:CA does not exist > try to run “csg_dump --top topol.xml” and check how VOTCA labels things.
Christoph > My topology file looks like:- > <topology base="temp.pdb"> > <molecules> > <clear/> > <define name="ALA" first="1" nbeads="13" nmols="250"/> > <define name="VAL" first="3251" nbeads="19" nmols="250"/> > </molecules> > </topology> > > My individual alanine and valine xml files are:- > Alanine- > <cg_molecule> > <name>ALA</name> > <ident>ALA</ident> > <topology> > <cg_beads> > <cg_bead> > <name>ALA</name> > <type>ALA</type> > <mapping>A</mapping> > <beads> > 1:ALA:CA 1:ALA:C 1:ALA:N 1:ALA:H1 1:ALA:H2 1:ALA:CB 1:ALA:HA > 1:ALA:HB1 1:ALA:HB2 1:ALA:HB3 1:ALA:O 1:ALA:OXT 1:ALA:HXT > </beads> > </cg_bead> > </cg_beads> > </topology> > <maps> > <map> > <name>A</name> > <weights>12 12 14 1 1 12 1 1 1 1 16 16 1</weights> > </map> > </maps> > </cg_molecule> > > Valine > <cg_molecule> > <name>VAL</name> > <ident>VAL</ident> > <topology> > <cg_beads> > <cg_bead> > <name>VAL</name> > <type>VAL</type> > <mapping>A</mapping> > <beads> > 1:VAL:CA 1:VAL:C 1:VAL:N 1:VAL:H1 1:VAL:H2 1:VAL:CB 1:VAL:HA > 1:VAL:CG1 1:VAL:HG11 1:VAL:HG12 1:VAL:HG13 1:VAL:CG2 1:VAL:HB 1:VAL:HG21 > 1:VAL:HG22 1:VAL:HG23 1:VAL:O 1:VAL:OXT 1:VAL:HXT > </beads> > </cg_bead> > </cg_beads> > </topology> > <maps> > <map> > <name>A</name> > <weights>12 12 14 1 1 12 1 12 1 1 1 12 1 1 1 1 16 16 1</weights> > </map> > </maps> > </cg_molecule> > > I have attached the pdb file for further reference. > > Can anyone please help me with this? > > -- > 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/3c0b76f3-ff3a-4013-8b74-d366e1e9c865n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/3c0b76f3-ff3a-4013-8b74-d366e1e9c865n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Christoph Junghans Web: http://www.compphys.de -- 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/CAHG27e7WZfOD2xdHy1AWWob7zNtdr5cBpYydNGp0WmA9sfqO9w%40mail.gmail.com.
