Re: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes?

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Tue Jul 27 2021 - 11:27:59 CDT

Hi Victor

Well, I know that to use NAMD in order to implement MD simulation with
Drude polarizable FF, CHARMM is needed to generate a CHARMM-compatible .psf
file. I don't have access to the CHARMM program and I decided to use
CHARMM-GUI. I posted the question in both the NAMD and CHARMM forum (link
<https://urldefense.com/v3/__https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=38310*Post38310__;Iw!!DZ3fjg!vAsj-JkznSgGwjgnTpVBZ3ZYPX0s9Fh4oUUVIlm7KE__ZocQ-LgBj8xQNx4V-MvMWQ$ >)
but nobody answered. It seems the CHARMM forum is not as active as the NAMD
one. I also posted the question in the VMD mailing list. Would be so
thankful if anybody could give me a hint..

All the best,
Zeynab

On Mon, Jul 26, 2021 at 7:31 PM Victor Kwan <vkwan8_at_uwo.ca> wrote:

> This is a CHARMM problem, isn't it?
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> zeynab hosseini <hosseinizeynab93_at_gmail.com>
> *Sent:* Sunday, July 25, 2021 3:07 PM
> *To:* NAMD list <namd-l_at_ks.uiuc.edu>
> *Subject:* namd-l: Does CHARMM-GUI Drude-Prepper input generator work for
> MD simulation of carbon nanotubes?
>
> 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
>

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