Physics

Dear all, I am trying to calculate the APL of my bilayer. It is heterogenous, but I have defined the atom triad following the default MEMBPLUGIN settings / as recommended by the wiki page. The calculation runs and outputs fine from frames 1 to 919. Then fails on frame 920 with the following error: Something went wrong. Command: lipidarea -structure step5_charmm2gmx.psf -trajectory step7all_every1ns_whole.xtc -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLPE SOPE DSPE SDPS SOPS SAPI25 PNPI25 POPI25"...

Thanks for the speedy response. Yes, that seems to be the case - apparently some atom names have been altered in the tails of SOPS such that they no longer follow conventional CHARMM atom names. I have generated a .psf for it and now it works as normal. Well spotted. Thanks so much again.

Hi all, I am experiencing similar errors as Thomas: Membrane SCD) Calculating Order parameters... Building topology... known residues: SDPS SOPS residue: SDPS assigning acyl chain id 2 according to C names assigning acyl chain id 3 according to C names index numbers appear to be correct has 2 acyl chains: chain id 2 with 22 carbon atoms chain id 3 with 18 carbon atoms residue: SOPS has no P headgroup, using name N as head instead Error: Something went wrong. Error: can't read "ntopo": no such variable...

Hi all, I am experiencing the similar errors as Thomas: Membrane SCD) Calculating Order parameters... Building topology... known residues: SDPS SOPS residue: SDPS assigning acyl chain id 2 according to C names assigning acyl chain id 3 according to C names index numbers appear to be correct has 2 acyl chains: chain id 2 with 22 carbon atoms chain id 3 with 18 carbon atoms residue: SOPS has no P headgroup, using name N as head instead Error: Something went wrong. Error: can't read "ntopo": no such...

Hi all, I am experiencing the similar errors as Thomas: Membrane SCD) Calculating Order parameters... Building topology... known residues: SDPS SOPS residue: SDPS assigning acyl chain id 2 according to C names assigning acyl chain id 3 according to C names index numbers appear to be correct has 2 acyl chains: chain id 2 with 22 carbon atoms chain id 3 with 18 carbon atoms residue: SOPS has no P headgroup, using name N as head instead Error: Something went wrong. Error: can't read "ntopo": no such...

Hi all, I am experiencing the similar errors as Thomas: Membrane SCD) Calculating Order parameters... Building topology... known residues: SDPS SOPS residue: SDPS assigning acyl chain id 2 according to C names assigning acyl chain id 3 according to C names index numbers appear to be correct has 2 acyl chains: chain id 2 with 22 carbon atoms chain id 3 with 18 carbon atoms residue: SOPS has no P headgroup, using name N as head instead Error: Something went wrong. Error: can't read "ntopo": no such...