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? 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 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 >>>>>> <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 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 > <https://groups.google.com/d/msgid/votca/CAHG27e4ypf5Po8_zKmhBSbSTW_xgGBu09Bmj6Nsh8KdQtYJN-Q%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. 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