Hi
I am working on simulating lipid bilayers with previtamin D. I have generated a CMAP for the open-ring portion of the previtamin D molecule and I want to apply it to my system.

The membrane contains a total of eight Pre molecules and I am unsure how to get the CMAP to apply to all the molecules and not just RESID 1. My assumption is that the !NCRTERM portion of step5_assembly.psf requires one line for each dihedral that will be modified by the CMAP, with the atom types identified in my ligand rtf file. If I have eight ligands then I should have eight lines.

The CHARMM output states that the additional cross-terms that I have defined do not have an associated CMAP. My confusion stems from the fact that the atoms I selected in the !NCRTERM block do not correspond to the same types shown in output. I used the atom indices from the psf file to select the atoms and in that file they have the correct type.

Ultimately what I am looking to find out is this: do I need a new cross-term for each separate ligand or will CHARMM recognize one cross-term and apply it to the other ligands for me? (Handling multiple cross-terms is not discussed in the prm portion of the user manual)


I have attached four files: the output from my attempted run, the coordinates and cross-term blocks from step5_assembly.psf (full file too large), and the rtf and prm file for my previtamin D ligand.

Also, below is a highlight showing how the atom labels are not corresponding with what I am expecting.

From cross-terms block of psf:
8 !NCRTERM: cross-terms
67 54 51 50 51 50 48 1
139 126 123 122 123 122 120 73
211 198 195 194 195 194 192 145
283 270 267 266 267 266 264 217
355 342 339 338 339 338 336 289
427 414 411 410 411 410 408 361
499 486 483 482 483 482 480 433
571 558 555 554 555 554 552 505

From atoms block psf:
139 HETA 2 LIG C20 CG321 -0.201000 12.0110 0 0.00000 -0.301140E-02
126 HETA 2 LIG C19 CG2DC1 0.190000E-01 12.0110 0 0.00000 -0.301140E-02
123 HETA 2 LIG C17 CG2DC2 -0.149000 12.0110 0 0.00000 -0.301140E-02
122 HETA 2 LIG C15 CG2DC2 -0.148000 12.0110 0 0.00000 -0.301140E-02
120 HETA 2 LIG C9 CG2DC1 0.350000E-01 12.0110 0 0.00000 -0.301140E-02
73 HETA 2 LIG C3 CG3RC1 -0.132000 12.0110 0 0.00000 -0.301140E-02


From output:
: No cross-term map for 2 ( CG321 HAL2 CTL2 HGA3 ) ( HGA1 HGA3 HGA1 HGA1 )
: No cross-term map for 3 ( HGA2 CG2DC1 HAL2 HGA2 ) ( HGA3 HGA2 HGA3 HGA2 )
: No cross-term map for 4 ( HGA3 HGA3 HGA3 PL ) ( HAL2 PL HAL2 CG321 )
: No cross-term map for 5 ( HGA2 HGA3 HGA2 CTL2 ) ( CTL3 CTL2 CTL3 HGA2 )
: No cross-term map for 6 ( CG321 HAL2 HGA3 HGA2 ) ( CG321 HGA2 HGA3 HGA3 )
: No cross-term map for 7 ( HGA4 CTL2 CTL2 CG321 ) ( CG3C52 CG321 CG3C52 CG3C51 )
: No cross-term map for 8 ( HGA3 HGA3 HAL2 CG2DC2 ) ( CG331 CG2DC2 CG331 HGA3 )
: A TOTAL OF 7 MISSING PARAMETERS

Attached Images
psf.txt (67.92 KB, 144 downloads)
SHA1: bd816fc495a07325e6a2d97693ddd0fa5d0bdafe
out.txt (93.73 KB, 184 downloads)
SHA1: 0df47a851bb012da25b3232a6562d03fe05e7c2b
cmap_prm.txt (22.13 KB, 143 downloads)
SHA1: ac725111365278fa852be14448550d95b736076a
rtf.txt (3.65 KB, 129 downloads)
SHA1: d5eea27928f3d0588bdf9db1e8e518bde6dfe7a8