VMD-L Mailing List

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Mon Jul 26 2021 - 14:08:52 CDT

Dear all,

I have the intention to perform molecular dynamics (MD) simulation of
carbon nanotubes (CNT) using the Drude polarizable force field implemented
in NAMD. I‌nitially, I used CHARMM-GUI to produce a solvated CNT inputs for
NAMD using Nanomaterial Modeler in CHARMM-GUI. I can run the MD simulation
(using non-polarizable FF) for this system. But as soon as I‌ use these
inputs (.pdb & .psf files) to produce Drude-Prepper inputs for MD
simulation of polarizable force field, I‌ receive a message mentioning
CHARMM was terminated abnormally with the following error. It seems that
the residue TUBE is not recognized. My question is how it is recognized
before (when performing MD with non-polarizable force field), but when it
comes to polarizable FF the TUBE residue is not recognized?

CHARMM was terminated abnormally.
Please check the output or report
<https://urldefense.com/v3/__https://charmm-gui.org/?doc=contact&jobid=2723850529__;!!DZ3fjg!vkacUvSVvdO9w26Z8SWQAEqxxFT0uUzW_mvwdBr0FerznRubI8nvh8uQOaWmvdEUaQ$>
this
failure to the CHARMM-GUI developers.
Output Excerpt from step2_drude.out:

 Comparing "NONE" and "CNEU".
 IF test evaluated as false. Skipping command

 CHARMM> if @cterpatch .eq. CT1 if @cname .eq. GLY set cterpatch CT1G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT1".
 IF test evaluated as false. Skipping command

 CHARMM> if @cterpatch .eq. CT2 if @cname .eq. GLY set cterpatch CT2G
 Parameter: CTERPATCH -> "NONE"
 Parameter: CNAME -> "TUBE"
 Comparing "NONE" and "CT2".
 IF test evaluated as false. Skipping command

 CHARMM>

 CHARMM> set gene = 0
 Parameter: GENE <- "0"

 CHARMM> if @type eq protein then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "PROTEIN".
 IF test evaluated as false. Skip to ELSE or ENDIF

 CHARMM>

 CHARMM> if @type eq rna then !UMB: explicitly for rna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "RNA".
 IF test evaluated as false. Skip to ELSE or ENDIF

 CHARMM>

 CHARMM> if @type eq dna then !UMB: explicitly for dna
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "DNA".
 IF test evaluated as false. Skip to ELSE or ENDIF

 CHARMM>

 CHARMM> if @type eq carb then
 Parameter: TYPE -> "ELSE"
 Comparing "ELSE" and "CARB".
 IF test evaluated as false. Skip to ELSE or ENDIF

 CHARMM>

 CHARMM> if gene .eq. 0 then
 Comparing "0" and "0".
 IF test evaluated as true. Performing command

 CHARMM> ! default generate if not protein or water

 CHARMM> generate @segname first none last none setup warn
drude dmass 0.4 ! show
 Parameter: SEGNAME -> "NM"
 Drude polarizability will be setup for SEGID: NM mass of Drudes
particles = 0.4000

 ***** ERROR in GENIC ***** Residue 'TUBE ' was not found.

                            /---------\
                           / \
                          / \
                         / \
                         ! XXXX XXXX !
                         ! XXXX XXXX !
                         ! XXX XXX !
                         ! X !
                          --\ XXX /--
                           ! ! XXX ! !
                           ! ! ! !
                           ! I I I I I !
                           ! I I I I !
                            \ /
                             -- --
                               \---/
                        XXX XXX
                       XXXX XXXX
                       XXXXX XXXXX
                          XXX XXX
                            XXX XXX
                               XXXXX
                              XXX XXX
                            XXX XXX
                          XXX XXX
                       XXXXX XXXXX
                       XXXX XXXX
                        XXX XXX

 Execution terminated due to the detection of a fatal error.

                    ABNORMAL TERMINATION
                    MOST SEVERE WARNING WAS AT LEVEL 1

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME: 2.11 SECONDS
                         CPU TIME: 2.11 SECONDS

All the Best,
Zeynab