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Parameter Set Discussion Jump to new posts
topology file for cobalt oxide Chrameh Mbah 08/05/21 07:21 PM
Hello,
Please can someone direct me to where I can find a topology file for cobalt oxide.
0 7 Read More
CHARMM-GUI Jump to new posts
Re: Meaning of BB and SC in DPOSRES_FC_ yarasayed 07/27/21 11:04 PM
I believe now that BB stands for Backbone and SC stands for side chains. Both referring to a protein in the system and the constraint command is present in the mdp files whether there is an actual protein in the system or not.
Hope this is helpful.
1 77 Read More
CHARMM-GUI Jump to new posts
Distance in Multicomponent Assembler yarasayed 07/26/21 11:17 PM
Dears,

Can I dictate the distance at which a small organic molecule is placed from a membrane in CHARMM-GUI's Multicomponent Assembler?
And if I can't, how can I calculate or get the distance at which the molecule was automatically placed?
0 24 Read More
CHARMM-GUI Jump to new posts
How can I add a lipid molecule to CHARMM-GUI's list? yarasayed 07/26/21 11:07 PM
Dears,

I need to simulate a molecule that is not available in CHARMM-GUI's membrane builder list.
It is a sphingomyelin head-group with two identical acyl chains of 18:0.
How can I possibly do that?
0 19 Read More
CHARMM-GUI Jump to new posts
CHARMM-GUI Drude-Prepper input generator for CNTs Zeynab Hosseini 07/26/21 07:45 PM
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
0 22 Read More
Parameter Set Discussion Jump to new posts
Re: Selenium containing ligand an_a 07/24/21 01:11 AM
rmv,

Thank you very much for sharing this nice idea from the paper. This is perhaps what I will do as well. Seems like Se parameters are not available in many of the popular forcefields.

ana
2 73 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Counter-ions and PME rmv 07/20/21 06:00 PM
Peptides and proteins can have a range of net charge values, so adding counterions to achieve a net zero charge for the entire system is fairly standard practice. I generally add ca. 100 mM excess salt, so that outcome is less sensitive to initial ion placement. I agree about avoiding constant pH methods.
3 114 Read More
Installation and Testing Jump to new posts
cmake/openmm: CUDA_BIN_PATH mspichty 07/13/21 01:44 PM
Hi, all!

For the compilation of c45b2 with cmake and CUDA/OpenMM-support it is necessary (at least on oour supercomputer center) to declare the environment variable CUDA_BIN_PATH in addition to CUDATK and OPENMM_PLUGIN_DIR.
This information is missing in the documentation and would have been helpful....

Best,
Martin
0 55 Read More
Parameter Set Discussion Jump to new posts
Re: Parametrizing ligand bound to lysine by Schiff Base rmv 07/09/21 09:39 PM
Which web site are you referring to?

If it is charmm-gui, there is a forum for that here, but most questions posted go unanswered lately, as they prefer that people use the Contact page on the charmm-gui site.

Importing ligands which may or may not be be well defined in the CHARMM force fields can be an exercise fraught with peril. You should probably start with the CGenFF site; there are some useful posts in the Parameter forum, and a paper or two.
1 66 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Langevin dynamics termination rmv 07/07/21 04:17 PM
There's no way to say anything from the limited information provided. There may be some hints in the output log file; you should look for them.
1 77 Read More
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