A List of Solutions to Some WARNINGs in CHARMM Simulation Package

Molecular Dynamics

Home

Syndication

1. "Element negative. No operation" from the SCALAR module

e.g.

CHARMM>    scalar sca4 sum sca5 ! + <y^2>

CHARMM>    scalar sca4 sum sca2 ! - <y>^2

CHARMM>    scalar sca4 sum sca6 ! + <z^2>

CHARMM>    scalar sca4 sum sca3 ! - <z>^2

CHARMM>    scalar sca4 sqrt

      ***** LEVEL 0 WARNING FROM <SCALAR> *****
      ***** Element negative. No operation
      ******************************************
      BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

[[ Solution ]]: This is most likely due to the fact that some atoms' coordinates are missing somehow. Try to find out these atoms and fill their internal coordinates.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

2. "zero selection specified" when using HBUILD

e.g.

CHARMM>    !Rebuild hydrogen coordinates
CHARMM>    HBUIld SELE ALL END
SELRPN>    667 atoms have been selected out of    667

      ***** LEVEL 4 WARNING FROM <GTHBUI> *****
      ***** Zero selection specified
      ******************************************
      BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

[[ Solution ]]: change the selection to hydrogen atoms only, i.e.

CHARMM>    !Rebuild hydrogen coordinates
CHARMM>    HBUIld SELE hydrogen END
SELRPN>    344 atoms have been selected out of    667
PRNHBD: CUToff Hydrogen Bond distance =    0.5000   Angle =   90.0000
         CuT switching ON HB dist. =     3.5000 OFf HB dist. =    4.0000
         CuT switching ON Hb Angle =    50.0000 OFf Hb Angle =   70.0000
         ACCEptor antecedents included
         All hydrogen bonds for each hydrogen will be found
         Hydrogen bonds between excluded atoms will be kept

[[ Reason ]]: (from CHARMM hbuild.doc)

"<atom-selection> specify the hydrogens to be (re-)constructed."

"By default (if no selection is specified) these are all unknown hydrogens and lone pairs (this is equivalent to a selection "SELEction (LONE .OR. HYDRogen) .AND..NOT INITial")."

[[ Remarks ]]: What is said in hbuild.doc may be true. However, if one does not make any selections after the HBUILD keyword, the same warning will still appear.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

3. "Failed to allocate memory for natomingp, gptoalst" from gbsw.src

e.g.

***** LEVEL -1 WARNING FROM <GB_lookup>gbsw.src *****
      ***** Failed to allocate memory for natomingp,gptoalst
      ******************************************
      BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

[[ Solution ]]; Most likely this is due to the missing coordinates for some atoms. Try to find these atoms and fill their coordinates.

4. "Zero length string being converted to 0" from PHMD

e.g.

CHARMM>    label PERLDONE

CHARMM>    phmd par 23 wri 25 ph 7.0 npri 100 mass 10 barr 1.75 bartau 2 temp 300 lam sele .not. ( resn TIP3 .or. RESN CLA .or. RESN SOD ) end

PHMD> Continous constant pH molecular dynamics

SELRPN>     36 atoms have been selected out of   2163
TITLE> * STATES FILE FOR HYBRID-PHMD
TITLE> * SYNTAX:
TITLE> * RESNAME MODEL_PKA PARA PARB
TITLE> * ATOM_TYPE CHARGE(1) CHARGE(2) [RAD(1) RAD(2)]
TITLE> *
WARNING from DECODF -- Zero length string being converted to 0.
PHMD> Grp # 1:ARG (ARG    1) pKa= 12.50 Prot
PHMD> Grp # 1:ARG (ARG    1) HH12

[[ Solution ]]: double check the phmd titration parameter file. Most likely its format is not correct, e.g. leaving out the barrier potential.

results:

CHARMM>    phmd par 23 wri 25 ph 7.0 npri 100 mass 10 barr 1.75 bartau 2 temp 300 lam sele .not. ( resn TIP3 .or. RESN CLA .or. RESN SOD ) end

PHMD> Continous constant pH molecular dynamics

SELRPN>     36 atoms have been selected out of   2163
TITLE> * STATES FILE FOR HYBRID-PHMD
TITLE> * SYNTAX:
TITLE> * RESNAME MODEL_PKA PARA PARB BARR
TITLE> * ATOM_TYPE CHARGE(1) CHARGE(2) [RAD(1) RAD(2)]
TITLE> *
PHMD> Grp # 1:ARG (ARG    1) pKa= 12.50 Prot
PHMD> Grp # 1:ARG (ARG    1) HH12
%%%%%%%%%%%%%%%%%%%%%%%%%%%%

e.g.

CHARMM>    label PERLDONE

CHARMM>    nbond elec atom cdie shift vdw vswitch ctonnb 10.0 ctofnb 12.0 cutnb 14.0 cutim 14.0 inbfrq -1 imgfrq -
1 ewald pmew fftx 64 ffty 64 fftz 64 kappa .34 spline order 6
<PME> Total heap storage needed =     1034887
Fill Ewald table: Number of points=     10000 EWXmax=    4.250000
fill erfc table: linear inter has rms error = 0.979220D-08 maximum error = 0.218740D-07
fill erfc table: cubic spline has rms error = 0.360331D-11 maximum error = 0.108438D-10

NONBOND OPTION FLAGS:
     ELEC     VDW      ATOMs    CDIElec SHIFt    VATOm    VSWItch
     BYGRoup NOEXtnd EWALd
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
WMIN   = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS    = 1.000
NBXMOD =      5
PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6
FFTX= 64 FFTY= 64 FFTZ= 64
                Using Pub FFT
                Real-to-Complex FFT
There are        0 atom pairs and        0 atom exclusions.
There are        0 group pairs and        0 group exclusions.
<MAKINB> with mode   5 found 27483 exclusions and   2472 interactions(1-4)
<MAKGRP> found    733 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 7400454 ATOM PAIRS AND        0 GROUP PAIRS
VEHEAP> Expanding heap size by        11436032 words.
== PRIMARY == SPACE FOR 11100701 ATOM PAIRS AND        0 GROUP PAIRS
VEHEAP> Expanding heap size by        16990208 words.
== PRIMARY == SPACE FOR 16651072 ATOM PAIRS AND        0 GROUP PAIRS

General atom nonbond list generation found:
11314422 ATOM PAIRS WERE FOUND FOR ATOM LIST
   641446 GROUP PAIRS REQUIRED ATOM SEARCHES

**** Warning **** The following extraneous characters
were found while command processing in CHARMM
CUTIM 14.0 IMGFRQ -1

There are many types of warnings that appear in CHARMM. Here are the possible solutions for some of them.

1. "Element negative. No operation" from the SCALAR module

e.g.

CHARMM>    scalar sca4 sum sca5 ! + <y^2>

CHARMM>    scalar sca4 sum sca2 ! - <y>^2

CHARMM>    scalar sca4 sum sca6 ! + <z^2>

CHARMM>    scalar sca4 sum sca3 ! - <z>^2

CHARMM>    scalar sca4 sqrt

      ***** LEVEL 0 WARNING FROM <SCALAR> *****
      ***** Element negative. No operation
      ******************************************
      BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

[[ Solution ]]: This is most likely due to the fact that some atoms' coordinates are missing somehow. Try to find out these atoms and fill their internal coordinates.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

2. "zero selection specified" when using HBUILD

e.g.

[[ Solution ]]: change the selection to hydrogen atoms only, i.e.

[[ Reason ]]: (from CHARMM hbuild.doc)

"<atom-selection> specify the hydrogens to be (re-)constructed."

"By default (if no selection is specified) these are all unknown hydrogens and lone pairs (this is equivalent to a selection "SELEction (LONE .OR. HYDRogen) .AND..NOT INITial")."

[[ Remarks ]]: What is said in hbuild.doc may be true. However, if one does not make any selections after the HBUILD keyword, the same warning will still appear.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

3. "Failed to allocate memory for natomingp, gptoalst" from gbsw.src

e.g.

[[ Solution ]]; Most likely this is due to the missing coordinates for some atoms. Try to find these atoms and fill their coordinates.

4. "Zero length string being converted to 0" from PHMD

e.g.

[[ Solution ]]: double check the phmd titration parameter file. Most likely its format is not correct, e.g. leaving out the barrier potential.

results:

5. "extraneous characters" from NBOND settings

e.g.

[[ Comments ]]: CUTIM should not appear in NBOND settings . The actual value of CUTIm should be calculated by "crystal build" based on the information on the water box dimensions (see below).

[[ Solution ]]: Thus CUTIM should be removed from the NBOND settings and IMGFRQ can be kept. After this modification, no more warning is issued.

CHARMM>    label PERLDONE

CHARMM>    crystal defined octa 70.488 70.488 70.488 109.4712206344907 109.4712206344907 109.4712206344907
Crystal Parameters : Crystal Type = OCTA
           A     =   70.48800 B    =   70.48800 C     =   70.48800
           Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122

CHARMM>    label PERLDONE

CHARMM>    crystal build cutoff 35.244 noper 0
XBUILD> Building all transformations with a minimum atom-atom
         contact distance of less than   35.24 Angstroms.

Range of Grid Search for Transformation     1 :
Lattice Vector A    -3 TO     3
Lattice Vector B    -3 TO     3
Lattice Vector C    -2 TO     2

Note: the actual value of CUTIm is 35.244 in this case.

   NSTEP =      500    NSAVC =      500    NSAVV =        0
ISCALE =        0   ISCVEL =        0   IASORS =        1
IASVEL =        1   ICHECW =        1   NTRFRQ =      500
IHTFRQ =        0   IEQFRQ =       50   NPRINT =      500
INBFRQ =       -1   IHBFRQ =        0   IPRFRQ =      500
ILBFRQ =       50   IMGFRQ =       -1    ISEED =          2023018546
Note: the value for IMGFRQ is "-1".

%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Posted 05-17-2010 1:40 PM by StevenWang

Filed under: CHARMM

Comments

guangdianzi3 wrote re: A List of Solutions to Some WARNINGs in CHARMM Simulation Package

on 05-31-2010 11:39 PM

Hi,

I have a problem regarding to GBSW solvation model.

I got a warning saying

***** LEVEL -4 WARNING FROM <GB_Solv1>gbsw.src *****

***** Array boundaries exceeded: sfprod0vdw

Do you have any idea what is wrong?

Previous I have seen this because the protein constains a phosphate group which doesn't have parameter in CHARMM22 ff.

But this time, the protein only have quite normal protein residues.

guangdianzi3 wrote re: A List of Solutions to Some WARNINGs in CHARMM Simulation Package

on 06-07-2010 12:34 AM

done. It is a problem of compilation. I changed from pgi 7 to pgi 9.

Syndication

Recent Posts

Tags

Archives

1. "Element negative. No operation" from the SCALAR module

2. "zero selection specified" when using HBUILD

1. "Element negative. No operation" from the SCALAR module

2. "zero selection specified" when using HBUILD

Comments