From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Thu Jul 29 2021 - 10:36:23 CDT
Hi Michael,
I really appreciate your help. I'll try it..
All the best,
Zeynab
On Wed, Jul 28, 2021 at 9:57 PM Michael Robinson <
michael.robinson1_at_monash.edu> wrote:
> 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
>>>
>>
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST