What you're doing looks basically ok. I admit I haven't looked in great detail.
This complaint from leap is what you need to work on:
!FATAL ERROR----------------------------------------
!FATAL: In file [varArray.c], line 182
!FATAL: Message: Realloc: Cannot allocate memory!
!ABORTING.
My experience is that this sort of thing is due to some sort of
formatting issue in one or more of the files.
It is tempting to say the issue is in the DIHE lines, but it could be
something before that.
Try making the smallest version of the system that you can. Add,
remove and change things until you figure it out.
One low-hanging thing to check: these files are column-delimited.
Pay particular attention to the number of spaces between entries.
Compare your spacing with files that are known to work.
I'm sorry I can't be more helpful. Were you able to fix it already?
If so, what did you do?
On Thu, May 7, 2020 at 4:31 AM Vijay Achari <glycoamber.gmail.com> wrote:
>
> Dear AMBER experts,
>
> I am trying to develop AMBER topology file for a simple glycolipid (glucose
> attached with alkyl chain)
>
> 1) I modelled the glycolipid.
>
> 2) I used antechamber to get prepin file using below command
> antechamber -fi pdb -fo prepi -i glycoglu.pdb -o glycoglu.prepi -rn GLU -c
> bcc -pf y -s 2
>
> Below I shared a fraction of the prepin file I get . .
> ___________________________________________________
> 0 0 2
>
> This is a remark line
> molecule.res
> GLU INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
> 4 O16 oh M 3 2 1 1.540 111.208 -180.000 -0.603800
> 5 H22 ho E 4 3 2 0.981 52.492 99.995 0.424000
> 6 C07 c3 M 4 3 2 1.438 87.250 -13.485 0.088100
> 7 H12 h1 E 6 4 3 1.094 109.205 -3.410 0.078700
> 8 C06 c3 M 6 4 3 1.555 109.011 -122.325 0.109100
> 9 H11 h1 E 8 6 4 1.094 109.351 -54.466 0.061700
> 10 O15 oh S 8 6 4 1.438 110.511 65.548 -0.603800
> 11 H21 ho E 10 8 6 0.980 106.655 -66.557 0.426000
> 12 C05 c3 M 8 6 4 1.555 110.222 -173.930 0.120100
> 13 O02 oh S 12 8 6 1.438 110.276 171.603 -0.596800
> 14 H01 ho E 13 12 8 0.981 106.683 65.702 0.426000
> 15 H10 h1 E 12 8 6 1.094 108.988 -68.508 0.078700
> 16 C04 c3 M 12 8 6 1.558 110.107 51.145 0.110100
> 17 H09 h1 E 16 12 8 1.094 109.248 65.203 0.060700
> 18 C14 c3 3 16 12 8 1.552 111.553 -175.655 0.140400
> 19 H18 h1 E 18 16 12 1.092 109.706 -59.527 0.061700
> 20 O19 oh S 18 16 12 1.435 110.668 61.594 -0.596800
> 21 H23 ho E 20 18 16 0.981 105.874 -179.601 0.414000
> 22 H20 h1 E 18 16 12 1.092 109.013 -178.348 0.061700
> 23 O03 os M 16 12 8 1.442 110.854 -55.492 -0.451600
> 24 C08 c3 M 23 16 12 1.442 111.775 62.596 0.308900
> 25 H17 h2 E 24 23 16 1.093 110.442 56.456 0.052700
> 26 O13 os M 24 23 16 1.442 109.096 176.981 -0.424600
> 27 C24 c3 M 26 24 23 1.439 111.620 -70.286 0.135400
> 28 H33 h1 E 27 26 24 1.092 109.921 -57.841 0.038700
> 29 H34 h1 E 27 26 24 1.092 110.275 62.805 0.038700
> 30 C25 c3 M 27 26 24 1.549 108.841 -177.256 -0.085400
> 31 H35 hc E 30 27 26 1.092 109.024 -63.337 0.055200
> 32 H36 hc E 30 27 26 1.093 108.729 55.126 0.055200
> .
> .
> _____________________________________________________
>
> 3) I used GLYCAM_06j-1.prep, GLYCAM_06j.dat and lipid17.dat to re-name the
> atomtypes in my current prepin file.
>
> Below I share the fraction of the prepin file that I renamed the atomtypes.
> ______________________________________________________
> 0 0 2
>
> This is a remark line
> molecule.res
> GLU INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
> 4 O16 Oh M 3 2 1 1.540 111.208 -180.000 -0.603800
> 5 H22 Ho E 4 3 2 0.981 52.492 99.995 0.424000
> 6 C07 Cg M 4 3 2 1.438 87.250 -13.485 0.088100
> 7 H12 H1 E 6 4 3 1.094 109.205 -3.410 0.078700
> 8 C06 Cg M 6 4 3 1.555 109.011 -122.325 0.109100
> 9 H11 H1 E 8 6 4 1.094 109.351 -54.466 0.061700
> 10 O15 Oh S 8 6 4 1.438 110.511 65.548 -0.603800
> 11 H21 Ho E 10 8 6 0.980 106.655 -66.557 0.426000
> 12 C05 Cg M 8 6 4 1.555 110.222 -173.930 0.120100
> 13 O02 Oh S 12 8 6 1.438 110.276 171.603 -0.596800
> 14 H01 Ho E 13 12 8 0.981 106.683 65.702 0.426000
> 15 H10 H1 E 12 8 6 1.094 108.988 -68.508 0.078700
> 16 C04 Cg M 12 8 6 1.558 110.107 51.145 0.110100
> 17 H09 H1 E 16 12 8 1.094 109.248 65.203 0.060700
> 18 C14 Cg 3 16 12 8 1.552 111.553 -175.655 0.140400
> 19 H18 H1 E 18 16 12 1.092 109.706 -59.527 0.061700
> 20 O19 Oh S 18 16 12 1.435 110.668 61.594 -0.596800
> 21 H23 Ho E 20 18 16 0.981 105.874 -179.601 0.414000
> 22 H20 H1 E 18 16 12 1.092 109.013 -178.348 0.061700
> 23 O03 Os M 16 12 8 1.442 110.854 -55.492 -0.451600
> 24 C08 Cg M 23 16 12 1.442 111.775 62.596 0.308900
> 25 H17 H2 E 24 23 16 1.093 110.442 56.456 0.052700
> 26 O13 Os M 24 23 16 1.442 109.096 176.981 -0.420600
> 27 C24 cA M 26 24 23 1.439 111.620 -70.286 0.135400
> 28 H33 hA E 27 26 24 1.092 109.921 -57.841 0.038700
> 29 H34 hA E 27 26 24 1.092 110.275 62.805 0.038700
> 30 C25 cA M 27 26 24 1.549 108.841 -177.256 -0.085400
> 31 H35 hA E 30 27 26 1.092 109.024 -63.337 0.055200
> 32 H36 hA E 30 27 26 1.093 108.729 55.126 0.055200
> .
> .
> ________________________________________________________-
>
> 4) When I run parmcheck I get warning and no frcmod file generated
>
> Below is the output I get....( I showed only the fraction of it..)
>
> parmchk2 -f prepi -i glycoglu.prepi -o glu.frcmod
> Warning: Atom type (Oh) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
> Warning: No mass information for atom type (Oh); set to 0.0.
> It is recommended to add the new atom type (Oh) to PARMCHK.DAT.
> Warning: Atom type (Ho) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
> Warning: No mass information for atom type (Ho); set to 0.0.
> It is recommended to add the new atom type (Ho) to PARMCHK.DAT.
> Warning: Atom type (Cg) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
> Warning: No mass information for atom type (Cg); set to 0.0.
> It is recommended to add the new atom type (Cg) to PARMCHK.DAT.
> Warning: Atom type (Os) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
> Warning: No mass information for atom type (Os); set to 0.0.
> It is recommended to add the new atom type (Os) to PARMCHK.DAT.
>
>
> 5) When I load the my pdb in xleap using below commands..
>
> source leaprc.gaff
> source leaprc.water.tip3p
> source leaprc.GLYCAM_06j-1
> source leaprc.lipid17
> loadamberprep glycoglu.prepi
> loadamberparams glu.frcmod
>
> 6) In the xleap, unit checking, I get message as below..
>
> ________________________________________________________
> Welcome to LEaP!
> Sourcing: ./amber_source.dat
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.gaff
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
> done
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/GLYCAM_06j.dat
> Reading title:
> GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
> Loading Prep file:
> /usr/local/INSTALL/amber18/dat/leap/prep/GLYCAM_06j-1.prep
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_amino_06j_12SB.lib
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/solvents.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/atomic_ions.lib
> Loading parameters:
> /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> Loading Prep file: ./start00_glu.prepin
> Loading parameters: ./glu.frcmod
> Reading title:
> > ll =loadpdb start00_glu.pdb
> Loading PDB file: ./start00_glu.pdb
> total atoms in file: 48
> > check ll
> Checking 'll'....
> Checking parameters for unit 'll'.
> Checking for bond parameters.
>
> Error: Could not find bond parameter for: Os - c3
>
> Error: Could not find bond parameter for: C3 - H2
>
> Error: Could not find bond parameter for: C3 - Os
>
> Error: Could not find bond parameter for: Os - C3
>
> Error: Could not find bond parameter for: Cg - C3
> Checking for angle parameters.
>
> Error: Could not find angle parameter: Os - c3 - h1
>
> Error: Could not find angle parameter: Os - c3 - h1
>
> Error: Could not find angle parameter: Os - c3 - c3
>
> Error: Could not find angle parameter: H2 - C3 - Os
>
> Error: Could not find angle parameter: C3 - Os - c3
>
> Error: Could not find angle parameter: Os - C3 - H2
>
> Error: Could not find angle parameter: Os - C3 - Os
>
> Error: Could not find angle parameter: Cg - Os - C3
>
> Error: Could not find angle parameter: Cg - Cg - C3
>
> Error: Could not find angle parameter: H1 - Cg - C3
>
> Error: Could not find angle parameter: Cg - C3 - Os
>
> Error: Could not find angle parameter: Cg - C3 - H2
>
> Error: Could not find angle parameter: Cg - C3 - Os
>
> Error: Could not find angle parameter: Oh - Cg - C3
>
> Warning: There are missing parameters.
> Unit is OK.
> _____________________________________________-
>
> 7) I than built a frcmod file with the bond length and angle parameters
> taken from GLYCAM06j.dat and lipid17.dat. I generated the frcmod file with
> the contents as below:
>
> Remark line goes here
> MASS
> Os 16.000 0.000
> cA 12.010 0.000
> Cg 12.010 0.000
> hA 1.008 0.000
>
> BOND
> Os-cA 320.00 1.410
>
> ANGLE
> hA-cA-Os 50.800 109.780 same as h1-c3-os, penalty score= 0.0
> cA-cA-Os 68.000 107.970 same as c3-c3-os, penalty score= 0.0
> Cg-Os-cA 38.0 107.0
>
> DIHE
> Os-cA-cA-hA 1 0.1600 0.00 3.00
> Os-cA-cA-cA 1 0.1800 0.00 -3.00
>
> IMPROPER
>
> NONBON
> IMPROPER
>
> NONBON
>
> __________________________________________________________
>
> I get error as below
>
> Welcome to LEaP!
> Sourcing: ./amber_source.dat
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.water.tip3p
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.water.tip3p
> done
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/atomic_ions.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/solvents.lib
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> This is the additional/replacement parameter set for TIP3P water
> Loading parameters:
> /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> Loading parameters:
> /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.ions234lm_126_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water
> model (12-6 normal usage set)
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
> done
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/GLYCAM_06j.dat
> Reading title:
> GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
> Loading Prep file:
> /usr/local/INSTALL/amber18/dat/leap/prep/GLYCAM_06j-1.prep
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_amino_06j_12SB.lib
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/solvents.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/atomic_ions.lib
> Loading parameters:
> /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.lipid17
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.lipid17 done
> Log file: ./leap.log
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/lipid17.dat
> Reading title:
> AMBER Lipid17 v1.1 Force Field, A. Skjevik, C. Dickson, B. Madej, I.R.
> Gould, R.C. Walker*
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/lipid17.lib
> Loading parameters: ./start00_glu.frcmod2
> Reading force field modification type file (frcmod)
> Reading title:
> Remark line goes here
> !FATAL ERROR----------------------------------------
> !FATAL: In file [varArray.c], line 182
> !FATAL: Message: Realloc: Cannot allocate memory!
> !ABORTING.
>
> 8) If i delete the DIHE lines from frcmod nad load again in xleap I get as
> bellow:
>
> Welcome to LEaP!
> Sourcing: ./amber_source.dat
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.water.tip3p
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.water.tip3p
> done
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/atomic_ions.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/solvents.lib
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> This is the additional/replacement parameter set for TIP3P water
> Loading parameters:
> /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> Loading parameters:
> /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.ions234lm_126_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water
> model (12-6 normal usage set)
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
> done
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/GLYCAM_06j.dat
> Reading title:
> GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
> Loading Prep file:
> /usr/local/INSTALL/amber18/dat/leap/prep/GLYCAM_06j-1.prep
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_amino_06j_12SB.lib
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib
> Loading library:
> /usr/local/INSTALL/amber18/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/solvents.lib
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/atomic_ions.lib
> Loading parameters:
> /usr/local/INSTALL/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> ----- Source: /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.lipid17
> ----- Source of /usr/local/INSTALL/amber18/dat/leap/cmd/leaprc.lipid17 done
> Log file: ./leap.log
> Loading parameters: /usr/local/INSTALL/amber18/dat/leap/parm/lipid17.dat
> Reading title:
> AMBER Lipid17 v1.1 Force Field, A. Skjevik, C. Dickson, B. Madej, I.R.
> Gould, R.C. Walker*
> Loading library: /usr/local/INSTALL/amber18/dat/leap/lib/lipid17.lib
> Loading parameters: ./start00_glu.frcmod4
> Reading force field modification type file (frcmod)
> Reading title:
> Remark line goes here
> Loading Prep file: ./start00_glu.prepin2
> > ll = loadpdb start00_glu.pdb
> Loading PDB file: ./start00_glu.pdb
> total atoms in file: 48
> > check ll
> Checking 'll'....
> Checking parameters for unit 'll'.
> Checking for bond parameters.
> Checking for angle parameters.
> Unit is OK.
> > saveamberparm ll xxx.top xxx.crd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
>
> Error: ** No torsion terms for Os-cA-cA-hA
> Error: ** No torsion terms for Os-cA-cA-hA
> Error: ** No torsion terms for Os-cA-cA-cA
> Error: ** No torsion terms for H2-Cg-Os-cA
> Error: ** No torsion terms for Cg-Os-cA-hA
> Error: ** No torsion terms for Cg-Os-cA-hA
> Error: ** No torsion terms for Cg-Os-cA-cA
> Error: ** No torsion terms for Os-Cg-Os-cA
> Error: ** No torsion terms for Cg-Cg-Os-cA
> Building improper torsion parameters.
> old PREP-specified impropers:
> total 0 improper torsions applied
> 0 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
> Warning: Parameter file was not saved.
> >
> _________________________________________________-
>
>
> My questions are relating to #7 and #8.
>
> Why I get FATAL error in #7 even though I used all given parameters ? I
> even adjusted the format of frcmod file
>
> How to combine GLYCAM06j.dat and lipid17.dat files to generate useful
> frcmod file?
>
> You help is much appreciated..
>
> Vijayan
> University Malaya.
> Malaysia.
> vijay.ramana.um.edu.my
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 10 2020 - 12:00:03 PDT
