On Wed, Jul 7, 2021 at 2:18 PM Rishabh Guha <[email protected]> wrote: > > Hey Christoph, > > First of all in my pdb file the atoms are at:- > ATOM 1 CA ALA A 1 11.853 -2.654 0.787 1.00 0.00 C > ATOM 2 C ALA A 1 12.896 -2.967 -0.276 1.00 0.00 C > > Do you know why votca is dividing all the positions by 10? VOTCA uses nm internally, and pdb is in Angstrom. > > Secondly these atoms show up as- > 0 Name 1:ALA:CA Type CA Mass 12.0107 Resnr 0 Resname ALA Charge 0 > 1 Name 1:ALA:C Type C Mass 12.0107 Resnr 0 Resname ALA Charge 0 > when I do csg_dump --top topology.xml and are mapped as 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 in the alanine.xml file. > > I do not see any issues in the mapping to be honest When you run csg_dump, what does it tell you the box size is?
Christoph > > Regards > > On Wed, Jul 7, 2021 at 4:09 PM Christoph Junghans <[email protected]> wrote: >> >> >> >> 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. >>>>>> >>>>>> -- >>>>>> 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. >>>>> >>>>> >>>>> >>>>> -- >>>>> 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. >>>> >>>> -- >>>> 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. >>> >>> >>> >>> -- >>> 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. >> >> -- >> 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/CAHG27e4ypf5Po8_zKmhBSbSTW_xgGBu09Bmj6Nsh8KdQtYJN-Q%40mail.gmail.com. > > > > -- > 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/CAFKQktBH-gARMiCQR%2BdJVudO95mHB5ZZkf6odZJDxmp6U2a-nQ%40mail.gmail.com. -- 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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