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Joined: Apr 2022
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Dear CHARMM-GUI developers and experts,
I want to run drude polarizable FF MD simulation in Amber20.
I've converted amber prmtop/inpcrd into psf/crd files with AmberTools21 (amb2chm_psf_crd.py).
With these psf/crd files I'm trying to generate files for drude polarizable MD simulation. But I'm getting the following error while using Charmm-GUI's drude preper.
It appears that there is some problem with the psf file, but since I'm very new to this tool. I don't have much idea about how to try and fix this.
Once the drude FF files are ready, I wish to use parmed's chamber option to write Amber prmtop/inpcrd files sot that I can run the MD simulation in Amber20 using drude FF.

I request you to please suggest to me the cause for the error and suggest changes that might fix it. Also please do comment if this approach to converting file formats is meaningful and expected to give the desired output.

Thanking you in advance and looking forward to hearing from the list soon.
Best regards, Vaibhav A. Dixit, NIPER Guwahati

Error with drude preper
JOB ID: 5085448035

Output Excerpt from step1_reader.out:
CHARMM> stream toppar/toppar_all36_label_fluorophore.str
VOPEN> Attempting to open::toppar/toppar_all36_label_fluorophore.str::
OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_label_fluorophore.str

INPUT STREAM SWITCHING TO UNIT 98
RDTITL> READ RTF CARD APPEND
RDTITL> No title read.
Parameter: IN1 <- ""

CHARMM> read rtf card append
MAINIO> Residue topology file being read from unit 98.
RDTITL> * TOPOLOGY FILES
RDTITL> *

CHARMM>

CHARMM> read param card flex append

PARAMETER FILE BEING READ FROM UNIT 98
RDTITL> * MINI FORCE FIELD PARAMETER FILE.
RDTITL> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM>

VCLOSE: Closing unit 98 with status "KEEP"

RETURNING TO INPUT STREAM 99

CHARMM>

CHARMM>

CHARMM>

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM>

CHARMM> ! Read PSF and Coordinates
CHARMM> open read unit 10 card name uploaded_files/1bvy-af-acd_out-dry.psf
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 10 with status "KEEP"
VOPEN> Attempting to open::uploaded_files/1bvy-af-acd_out-dry.psf::
OPNLGU> Unit 10 opened for READONLY access to uploaded_files/1bvy-af-acd_out-dry.psf

CHARMM> read psf unit 10 card
MAINIO> Protein structure file being read from unit 10.
PSFRD2> Reading PSF in the expanded format.
TITLE>
TITLE> *
Atom 1 0 N3 problem in psf

***** LEVEL -3 WARNING FROM *****
***** atom type not found for atom
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5



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-- --
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Execution terminated due to the detection of a fatal error.

ABNORMAL TERMINATION
MOST SEVERE WARNING WAS AT LEVEL -3

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 7.57 SECONDS
CPU TIME: 7.55 SECONDS

Joined: Sep 2003
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rmv Online Content
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The CHARMM-GUI developers no longer answer questions in the forums; please use their Contact on that site


Rick Venable
computational chemist


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