On Wed, Jul 7, 2021 at 13:44 Rishabh Guha <[email protected]> wrote: > Hey Christoph, > > Thanks for the help. I got to know about the csg_dump command as soon as I > sent you the email. For some reason, csg_dump is categorizing all the atoms > as the valine molecules as ALA as well, which is counterintuitive to me. > yeah, there is a way to fix this, these are just unique identifiers so it doesn’t matter a lot what they are as long as they are unique. This artifact mainly stems from the fact that the pdb format misses some molecule information.
> But I did change my valine.xml file to:- > > <cg_molecule> > <name>VAL</name> > <ident>VAL</ident> > <topology> > <cg_beads> > <cg_bead> > <name>VAL</name> > <type>VAL</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:CG1 1:ALA:HG11 1:ALA:HG12 1:ALA:HG13 1:ALA:CG2 1:ALA:HB 1:ALA:HG21 > 1:ALA:HG22 1:ALA:HG23 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 12 1 1 1 12 1 1 1 1 16 16 1</weights> > </map> > </maps> > </cg_molecule> > > Now, I get a different error, > I have 8000 beads in 500 molecules > I have 500 beads in 500 molecules for the coarsegraining > 1.1853 > -0.2654 > 0.0787 1.2896 > -0.2967 > -0.0276 > an error occurred: > coarse-grained bead is bigger than half the box > (atoms CA (id 1), C (id 2) , molecule 1) > > Can you please tell me what I can change? > this error means you are trying to map teo atoms that are more than half a box length away into one cg bead. The 6 number above are the positions. There can be multiple reasons for that error, most of the times it is a typo in the mapping file. If you are sure things are correct, you can always make the box bigger. Christoph > > > On Wed, Jul 7, 2021 at 3:29 PM Christoph Junghans <[email protected]> > wrote: > >> >> >> 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 a topic in the >> Google Groups "votca" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe. >> To unsubscribe from this group and all its topics, 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 >> <https://groups.google.com/d/msgid/votca/CAHG27e7WZfOD2xdHy1AWWob7zNtdr5cBpYydNGp0WmA9sfqO9w%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > > > -- > Rishabh Debraj Guha(PhD student) > > Graduate Research Assistant > Mechanical and Aerospace Engineering > North Carolina State University > Contact:- +1-347-205-2280 > > -- > 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/CAFKQktCXqB_zefYDpusjSBnLkt%2B77vfkgnU-dovocsFsiiKUow%40mail.gmail.com > <https://groups.google.com/d/msgid/votca/CAFKQktCXqB_zefYDpusjSBnLkt%2B77vfkgnU-dovocsFsiiKUow%40mail.gmail.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. 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