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
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Received on Thu May 07 2020 - 02:00:03 PDT
