From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Wed Jul 28 2021 - 20:57:29 CDT
Hi Zeynab,
I'm unfamiliar with the application of MD to carbon nanotubes, but I just
want to add that you no longer need to use CHARMM or CHARMM-GUI to generate
a Drude FF .psf file. Psfgen 2.0 was released last year, and can handle
structure preparation for the Drude force field in basically the same way
as a classical force field - see the latest user's guide:
https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf.
Psfgen 2.0 comes bundled with the latest alphas of VMD, and my local
installation of NAMD 2.14 is also reporting the use of psfgen 2.0.
Hopefully that's helpful!
Regards,
Michael Robinson
On Wed, 28 Jul 2021 at 02:37, zeynab hosseini <hosseinizeynab93_at_gmail.com>
wrote:
> 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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