VMD-L Mailing List

From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Tue Jul 27 2021 - 02:38:19 CDT

Sounds to me as if you should ask the charmm-gui people. Speaking
of someone who works with them quite a bit (but without experience with
the Drude prepper), they don't bite. Make sure to let them know the job ID
of your attempt (though as you can see, it is in the URL you sent).

Good luck,
Stefan

On Mon, Jul 26, 2021 at 03:08:52PM -0400, zeynab hosseini wrote:
> 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