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#37626 - 08/22/19 04:47 AM Fortran runtime error: Bad value during integer read
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 5
I made POPC input file through charmm-gui membrane builder , and I tried to running charmm " charmm -i step6.1_equilibration.inp" but it happen error.
As far as I know, the portran error is known by the unit setting, so in the step6.1_eqilibration.inp file

! Read PSF
open read unit 10 card name step5_assembly.psf
read psf unit 10 card

The unit has been adjusted(from 10 to 20). However, the same error still occurred.

How can I solve this situation?
please, Help me.

[sohyeon@theochem12 40popc]$ charmm -i step6.1_equilibration.inp
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 38a1 September 30, 2012
SVN revision
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-279.14.1.el6.x86_64(x86_64)@the
Created on 8/22/19 at 17:30:44 by user: sohyeon

Maximum number of ATOMS: 1000000, and RESidues: 333333
RDTITL> * GENERATED BY CHARMM-GUI ([url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG]HTTP://WWW.CHARMM-GUI.ORG[/url][/url][/url]) V2.0 ON AUG, 21. 2019. JOBID=156637331432
RDTITL> * INPUT FILES FOR EQUILIBRATION
RDTITL> *

CHARMM>

CHARMM> DIMENS CHSIZE 3000000 MAXRES 3000000
Size Original New
MAXA 1000000 3000000
MAXB 1000000 3000000
MAXT 2000000 6000000
MAXP 3000000 9000000
MAXIMP 500000 1500000
MAXNB 250000 750000
MAXPAD 1000000 3000000
MAXRES 333333 3000000
MAXSEG 125000 375000
MAXATC 500
MAXCB 1500
MAXCT 5500
MAXCP 10000
MAXCI 600
MAXCH 3200
MAXCN 125250
MAXCRT 333333 1000000

CHARMM>

CHARMM> ! Read topology and parameter files
CHARMM> stream toppar.str
VOPEN> Attempting to open::toppar.str::
OPNLGU> Unit 99 opened for READONLY access to toppar.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> * GENERATED BY CHARMM-GUI ([url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG]HTTP://WWW.CHARMM-GUI.ORG[/url][/url][/url]) V2.0 ON AUG, 21. 2019. JOBID=156637331432
RDTITL> * STREAM FILE FOR TOPOLOGY AND PARAMETER READING
RDTITL> *
Parameter: IN1 <- ""

CHARMM>

CHARMM> ! protein topology and parameter
CHARMM> !open read card unit 10 name toppar/top_all36_prot.rtf
CHARMM> !read rtf card unit 10
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36m_prot.prm
CHARMM> !read para card unit 20 flex
CHARMM>

CHARMM> ! nucleic acids
CHARMM> !open read card unit 10 name toppar/top_all36_na.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36_na.prm
CHARMM> !read para card unit 20 append flex
CHARMM>

CHARMM> ! carbohydrates
CHARMM> !open read card unit 10 name toppar/top_all36_carb.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36_carb.prm
CHARMM> !read para card unit 20 append flex
CHARMM>

CHARMM> ! lipids
CHARMM> open read card unit 10 name toppar/top_all36_lipid.rtf
VOPEN> Attempting to open::toppar/top_all36_lipid.rtf::
OPNLGU> Unit 10 opened for READONLY access to toppar/top_all36_lipid.rtf

CHARMM> read rtf card unit 10
MAINIO> Residue topology file being read from unit 10.
TITLE> * \\\\\\\ CHARMM36 ALL-HYDROGEN LIPID TOPOLOGY FILE ///////
TITLE> * ALL COMMENTS AND QUESTIONS SHOULD BE SUBMITTED TO THE
TITLE> * PARAMETER FORUM AT THE CHARMM WEBSITE: www.CHARMM.ORG
TITLE> *

CHARMM>

CHARMM> open read card unit 20 name toppar/par_all36_lipid.prm
VOPEN> Attempting to open::toppar/par_all36_lipid.prm::
OPNLGU> Unit 20 opened for READONLY access to toppar/par_all36_lipid.prm

CHARMM> read para card unit 20

PARAMETER FILE BEING READ FROM UNIT 20
TITLE> * \\\\\\\ CHARMM36 ALL-HYDROGEN LIPID PARAMETER FILE ///////
TITLE> * ALL COMMENTS AND QUESTIONS SHOULD BE SUBMITTED TO THE
TITLE> * PARAMETER FORUM AT THE CHARMM WEBSITE: www.CHARMM.ORG
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM>

CHARMM> ! CGENFF
CHARMM> !open read card unit 10 name toppar/top_all36_cgenff.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36_cgenff.prm
CHARMM> !read para card unit 20 append flex
CHARMM>

CHARMM> ! Interface FF
CHARMM> !open read card unit 10 name toppar/top_interface.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 10 name toppar/par_interface.prm
CHARMM> !read para card unit 10 append flex
CHARMM>

CHARMM> ! Additional topologies and parameters for water and ions
CHARMM> !stream toppar/toppar_water_ions.str
CHARMM> !stream toppar/toppar_dum_noble_gases.str
CHARMM>

CHARMM> ! Additional topologies and parameters for protein
CHARMM> !stream toppar/toppar_all36_prot_d_aminoacids.str
CHARMM> !stream toppar/toppar_all36_prot_fluoro_alkanes.str
CHARMM> !stream toppar/toppar_all36_prot_heme.str
CHARMM> !stream toppar/toppar_all36_prot_na_combined.str
CHARMM> !stream toppar/toppar_all36_prot_retinol.str
CHARMM> !stream toppar/toppar_all36_prot_stapling.str
CHARMM> !stream toppar/toppar_all36_prot_modify_res.str
CHARMM>

CHARMM> ! Additional topologies and parameters for nucleic acids
CHARMM> !stream toppar/toppar_all36_na_nad_ppi.str
CHARMM> !stream toppar/toppar_all36_na_rna_modified.str
CHARMM>

CHARMM> ! Additional topologies and parameters for lipids
CHARMM> !stream toppar/toppar_all36_lipid_bacterial.str
CHARMM> !stream toppar/toppar_all36_lipid_cardiolipin.str
CHARMM> !stream toppar/toppar_all36_lipid_cholesterol.str
CHARMM> !stream toppar/toppar_all36_lipid_inositol.str
CHARMM> !stream toppar/toppar_all36_lipid_lps.str
CHARMM> !stream toppar/toppar_all36_lipid_miscellaneous.str
CHARMM> !stream toppar/toppar_all36_lipid_model.str
CHARMM> !stream toppar/toppar_all36_lipid_prot.str
CHARMM> !stream toppar/toppar_all36_lipid_pyrophosphate.str
CHARMM> !stream toppar/toppar_all36_lipid_sphingo.str
CHARMM> !stream toppar/toppar_all36_lipid_yeast.str
CHARMM> !stream toppar/toppar_all36_lipid_hmmm.str
CHARMM> !stream toppar/toppar_all36_lipid_detergent.str
CHARMM> !stream toppar/toppar_all36_lipid_ether.str
CHARMM>

CHARMM> ! Additional topologies and parameters for carbohydrates
CHARMM> !stream toppar/toppar_all36_carb_glycolipid.str
CHARMM> !stream toppar/toppar_all36_carb_glycopeptide.str
CHARMM> !stream toppar/toppar_all36_carb_imlab.str
CHARMM>

CHARMM> ! Additional topologies and parameters for spin/fluorophore labels
CHARMM> !stream toppar/toppar_all36_label_spin.str
CHARMM> !stream toppar/toppar_all36_label_fluorophore.str
CHARMM>

CHARMM>

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM>

CHARMM> ! Read the system information
CHARMM> stream step3_size.str
VOPEN> Attempting to open::step3_size.str::
OPNLGU> Unit 99 opened for READONLY access to step3_size.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> SET BOXTYPE = RECT
RDTITL> No title read.
Parameter: IN1 <- ""

CHARMM> SET BOXTYPE = RECT
Parameter: BOXTYPE <- "RECT"

CHARMM> SET XTLTYPE = TETRAGONAL
Parameter: XTLTYPE <- "TETRAGONAL"

CHARMM> SET A = 52.2685374
Parameter: A <- "52.2685374"

CHARMM> SET B = 52.2685374
Parameter: B <- "52.2685374"

CHARMM> SET C = 85
Parameter: C <- "85"

CHARMM> SET ALPHA = 90.0
Parameter: ALPHA <- "90.0"

CHARMM> SET BETA = 90.0
Parameter: BETA <- "90.0"

CHARMM> SET GAMMA = 90.0
Parameter: GAMMA <- "90.0"

CHARMM> SET ZCEN = 0
Parameter: ZCEN <- "0"

CHARMM> SET NLIPTOP = 40
Parameter: NLIPTOP <- "40"

CHARMM> SET NLIPBOT = 40
Parameter: NLIPBOT <- "40"

CHARMM> SET WBOXZ = 22.5
Parameter: WBOXZ <- "22.5"

CHARMM> SET WATBOXZ = 22.5
Parameter: WATBOXZ <- "22.5"

CHARMM> SET NCHARGE = 0
Parameter: NCHARGE <- "0"

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM> stream step5_assembly.str
VOPEN> Attempting to open::step5_assembly.str::
OPNLGU> Unit 99 opened for READONLY access to step5_assembly.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> SET BOXTYPE = RECT
RDTITL> No title read.
Parameter: IN1 <- ""

CHARMM> SET BOXTYPE = RECT
Parameter: BOXTYPE <- "RECT"

CHARMM> SET XTLTYPE = TETRAGONAL
Parameter: XTLTYPE <- "TETRAGONAL"

CHARMM> SET A = 52.2685374
Parameter: A <- "52.2685374"

CHARMM> SET B = 52.2685374
Parameter: B <- "52.2685374"

CHARMM> SET C = 85
Parameter: C <- "85"

CHARMM> SET ALPHA = 90.0
Parameter: ALPHA <- "90.0"

CHARMM> SET BETA = 90.0
Parameter: BETA <- "90.0"

CHARMM> SET GAMMA = 90.0
Parameter: GAMMA <- "90.0"

CHARMM> SET ZCEN = 0.0
Parameter: ZCEN <- "0.0"

CHARMM> SET NLIPTOP = 40
Parameter: NLIPTOP <- "40"

CHARMM> SET NLIPBOT = 40
Parameter: NLIPBOT <- "40"

CHARMM> SET NWATER = 3596
Parameter: NWATER <- "3596"

CHARMM> SET POSID = POT
Parameter: POSID <- "POT"

CHARMM> SET NEGID = CLA
Parameter: NEGID <- "CLA"

CHARMM> SET NPOS = 0
Parameter: NPOS <- "0"

CHARMM> SET NNEG = 0
Parameter: NNEG <- "0"

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM>

CHARMM> ! Read PSF
CHARMM> open read unit 20 card name step5_assembly.psf
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 20 with status "KEEP"
VOPEN> Attempting to open::step5_assembly.psf::
OPNLGU> Unit 20 opened for READONLY access to step5_assembly.psf

CHARMM> read psf unit 20 card
MAINIO> Protein structure file being read from unit 20.
PSFRD2> Reading PSF in the expanded format.
TITLE> * GENERATED BY CHARMM-GUI ([url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG]HTTP://WWW.CHARMM-GUI.ORG[/url][/url][/url]) V2.0 ON AUG, 21. 2019. JOB
TITLE> * ASSEMBLE PREVIOUSLY GENERATED COMPONENTS (LIPID BILAYER, PROTEIN, PORE WATER,
TITLE> * DATE: 8/21/19 3:45:56 CREATED BY USER: apache
TITLE> *
At line 231 of file /home/yongbin/bin/c38a1_plumed/source/io/psfres.src (unit = 10, file = 'step5_assembly.psf')
Fortran runtime error: Bad value during integer read

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#37627 - 08/22/19 05:31 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Update to most recent CHARMM version.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37647 - 09/05/19 01:23 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 5
Thank you for your reply.

I used 3.8version, your comment means that I will download(install) version 41??


Edited by sohyeon (09/05/19 01:24 AM)

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#37650 - 09/05/19 04:59 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
www.charmm.org has information about obtaining CHARMM.
See http://charmm.chemistry.harvard.edu/charmm_lite.php for instructions on how to download the most recent freely available version of CHARMM.

Version 44b1 was released a couple of weeks ago. Version 41 is already 4 years old.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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