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Error while reading CHARMM36 parameter file
#37985 07/17/20 10:28 PM
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hawo Offline OP
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Hello everyone,
I downloaded and installed the recent version of CHARMM the other day, and I can't make it work with the CHARMM36 parameter file. An attempt to read file "charmm/toppar/par_all36_prot.prm" results in an error. Is there any way to resolve this? Thanks.

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Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Free Version 44b2 February 15, 2020
686801d1a
Copyright(c) 1984-2020 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-5.3.0-62-generic(x86_64)@hawo-machine
Created on 7/18/20 at 1:15:48 by user: hawo

Maximum number of ATOMS: 360720, and RESidues: 120240
bomblev -1
RDTITL> BOMBLEV -1

***** LEVEL 1 WARNING FROM *****
***** Title expected.
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

RDTITL> No title read.

***** LEVEL 1 WARNING FROM *****
***** Title expected.
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5


open unit 1 read card name top_all36_prot.rtf
CHARMM> open unit 1 read card name top_all36_prot.rtf
VOPEN> Attempting to open::top_all36_prot.rtf::
OPNLGU> Unit 1 opened for READONLY access to top_all36_prot.rtf

read rtf card unit 1
CHARMM> read rtf card unit 1
MAINIO> Residue topology file being read from unit 1.
TITLE> *>>>>>>>>CHARMM36 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>>> MAY 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *

close unit 1
CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

open unit 2 read card name par_all36_prot.prm
CHARMM> open unit 2 read card name par_all36_prot.prm
VOPEN> Attempting to open::par_all36_prot.prm::
OPNLGU> Unit 2 opened for READONLY access to par_all36_prot.prm

read param card unit 2
CHARMM> read param card unit 2

PARAMETER FILE BEING READ FROM UNIT 2
TITLE> *>>>> CHARMM36 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>>> FEB. 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
PARRDR> Error: Repeated ANGLE parameter ( 45123): NH2 CT2 CD
*** LEVEL -1 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.

Re: Error while reading CHARMM36 parameter file
hawo #37987 07/18/20 02:24 PM
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Have you modified the parameter file in any way?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Error while reading CHARMM36 parameter file
lennart #37989 07/18/20 06:23 PM
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hawo Offline OP
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No, I haven't modified the parameter file. That's the problem.

I think I found a workaround though: the error says "repeated angle parameter NH2 CT2 CD", so I removed the second record containing "NH2 CT2 CD" from the parameter file, and now it seems to work. But this feels like a band-aid rather than a solution, and it's probably something I shouldn't do.

Re: Error while reading CHARMM36 parameter file
hawo #37990 07/18/20 07:04 PM
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Where and when did you get the parameter file? This does not happen for me with par_all36_prot.prm from January 10, 2020.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Error while reading CHARMM36 parameter file
lennart #37991 07/18/20 10:07 PM
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hawo Offline OP
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My version is from March 18, 2020. I downloaded it along with the program from charmm.chemistry.harvard.edu a couple of days ago.

Re: Error while reading CHARMM36 parameter file
hawo #37992 07/18/20 10:29 PM
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rmv Online Content
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If I use the files from the toppar subdirectory of the c44b2 distribution (14 Feb 2020), I do get the error; the NH2 CT2 CD angle term is repeated in both par_all36_prot.prm and par_all36m_prot.prm, leading to the level -1 error. The term is also repeated in the files from the July 2019 bundle on the MacKerell lab web site (or was when I downloaded it a year ago).

The force constants and equilibrium angle are slightly different.

Update: The error does NOT occur if the FLEX keyword is used, e.g.

read param card flex name par_all36_prot.prm

In general, you should use the FLEX keyword, so this is not a major issue.

Last edited by rmv; 07/18/20 11:13 PM.

Rick Venable
computational chemist

Re: Error while reading CHARMM36 parameter file
rmv #37993 07/19/20 01:24 PM
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hawo Offline OP
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I see. Yes, it works now. Thanks.


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