On Wed, Jul 7, 2021, 14:05 Rishabh Guha <[email protected]> wrote: > Hey Christoph, > > Thanks for the pointers. I tried to look closely into my mapping files and > compared them with the pdb files, but nothing jumped out at me. Although I > admit that it can easily be an oversight-I have just started using > Votca today. I have attached all my files below. Does anything jump out at > you? I am convinced that none of my atoms are than half the box length away > The error says there is an atom at 1.1853 -0.2654 0.0787 and one at 1.2896 -0.2967 -0.0276 that you are trying to map in a cg bead. These are the ones you have to look at carefully in the mapping file.
Christoph > > Regards > > On Wed, Jul 7, 2021 at 3:55 PM Christoph Junghans <[email protected]> > wrote: > >> >> >> 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 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/CAHG27e6Kjvwxvv4suXuuqLSQ57AJeh_Vi-CepLi4A%3DXb9MmzWg%40mail.gmail.com >> <https://groups.google.com/d/msgid/votca/CAHG27e6Kjvwxvv4suXuuqLSQ57AJeh_Vi-CepLi4A%3DXb9MmzWg%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/CAFKQktBEGaPFAtudiU20y7Y-0pwe1jS2XXnvShd0kyXvfBLuOQ%40mail.gmail.com > <https://groups.google.com/d/msgid/votca/CAFKQktBEGaPFAtudiU20y7Y-0pwe1jS2XXnvShd0kyXvfBLuOQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- 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/CAHG27e4ypf5Po8_zKmhBSbSTW_xgGBu09Bmj6Nsh8KdQtYJN-Q%40mail.gmail.com.
