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 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