Hi,
I'm trying to create a small molecule with 4 dummy atoms that need extra parameters (for BOND, ANGLE and DIHEDRAL involving the dummy atoms). I'm using Glycam_06 forcefield and amber11 xLEaP/tleap version.
I try to do it by passing a parameters file to t/xLEaP, then save the library (file.lib) and create the topology (.top) and coordinate (.crd) files. I used to do this process quite often in the past using older versions of amber (amber7) but now, t/xleap is complainig every time. It is probably a silly detail but I cannot fix the problem. I follow the next steps:
1) I have the molecule in a Mol2 format file: lam0init.mol2
2) I have the extra parameters for Glycam_06 in the file: frcmod0
3) I try to run xLEaP / tleap using the file: leaprc
4) I get the next error message saying that missing parameters were found (but they should have been loaded in step 3!!!) and top/crd files were not created.
What am I doing wrong?
Thanks
Kepa K. Burusco
Files are shown hereafter:
1) lam0init.mol2
.<TRIPOS>MOLECULE
ROH
25 25 2 0 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 DHA 2.000001 1.000000 -0.000001 DH1 1 ROH 0.4450 ****
2 DOA 2.280678 1.918052 -0.000000 DO1 1 ROH -0.6390 ****
3 C1 1.131164 2.768651 -0.000004 CG 2 0GA 0.5090 ****
4 DOB 0.520206 2.576632 -0.896811 DO2 2 0GA 0.0000 ****
5 C2 1.627331 4.209621 -0.000001 CG 2 0GA 0.2460 ****
6 H2 0.762172 4.884143 -0.132455 H1 2 0GA 0.0000 ****
7 O2 2.518200 4.322900 -1.093502 OH 2 0GA -0.7130 ****
8 H2O 3.348918 3.896212 -0.884471 HO 2 0GA 0.4370 ****
9 C3 2.343417 4.524080 1.313840 CG 2 0GA 0.2860 ****
10 H3 3.259641 3.916832 1.376962 H1 2 0GA 0.0000 ****
11 O3 2.665653 5.906917 1.370127 OH 2 0GA -0.6990 ****
12 H3O 3.371246 6.087182 0.720343 HO 2 0GA 0.4270 ****
13 C4 1.492466 4.224950 2.470550 CG 2 0GA 0.2540 ****
14 H4 0.644544 4.925258 2.494970 H1 2 0GA 0.0000 ****
15 O4 2.256667 4.349342 3.672807 OH 2 0GA -0.7100 ****
16 H4O 1.906016 5.071400 4.195722 HO 2 0GA 0.4360 ****
17 C5 0.976315 2.789193 2.387034 CG 2 0GA 0.2830 ****
18 H5 1.832668 2.096982 2.479383 H1 2 0GA 0.0000 ****
19 O5 0.316337 2.557014 1.134139 OS 2 0GA -0.5740 ****
20 C6 -0.024167 2.446996 3.474795 CG 2 0GA 0.2760 ****
21 H61 -0.853404 3.154814 3.412949 H1 2 0GA 0.0000 ****
22 H62 0.425726 2.661942 4.447443 H1 2 0GA 0.0000 ****
23 O6 -0.511645 1.124819 3.370950 OH 2 0GA -0.6820 ****
24 H6O 0.004660 0.571625 3.953556 HO 2 0GA 0.4180 ****
25 DHB 0.104210 1.400781 -0.678665 DH2 2 0GA 0.0000 ****
.<TRIPOS>BOND
1 2 3 1
2 1 2 1
3 23 24 1
4 20 21 1
5 20 22 1
6 20 23 1
7 17 18 1
8 17 19 1
9 17 20 1
10 15 16 1
11 13 14 1
12 13 15 1
13 13 17 1
14 11 12 1
15 9 10 1
16 9 11 1
17 9 13 1
18 7 8 1
19 5 6 1
20 5 7 1
21 5 9 1
22 4 25 1
23 3 4 1
24 3 5 1
25 3 19 1
.<TRIPOS>SUBSTRUCTURE
1 ROH 1 **** 0 **** ****
2 0GA 3 **** 0 **** ****
2) frcmod0
Glucose parameters for lambda = 0.000000
MASS
DO1 16.00
DH1 1.008
DO2 1.008
DH2 1.008
BOND
DO2-DH2 553.0 0.960
DO1-DH1 553.0 0.960
CG-DO2 340.0 1.090
CG-DO1 320.0 1.430
ANGLE
OS-CG-DO2 60.00 110.00
CG-CG-DO2 45.00 111.00
DO1-CG-DO2 60.00 110.00
DO1-CG-CG 70.00 107.50
DO1-CG-OS 100.00 112.00
CG-DO2-DH2 55.00 109.50
CG-DO1-DH1 55.00 109.50
DIHE
DH2-DO2-CG-OS 1 0.00 0.0 0.00
DH2-DO2-CG-CG 1 0.00 0.0 0.00
DH2-DO2-CG-DO1 1 0.00 0.0 0.00
DO2-CG-OS-CG 1 0.60 0.0 -2.00
DO2-CG-OS-CG 1 0.10 0.0 3.00
DO2-CG-OS-CG 1 0.00 0.0 0.00
DO2-CG-CG-CG 1 0.15 0.0 3.00
DO2-CG-CG-OH 1 0.05 0.0 3.00
DO2-CG-CG-OH 1 0.00 0.0 0.00
DO2-CG-CG-OH 1 0.00 0.0 0.00
DO2-CG-CG-H1 1 0.17 0.0 3.00
DO2-CG-DO1-DH1 1 0.18 0.0 3.00
DH1-DO1-CG-CG 1 0.18 0.0 3.00
DH1-DO1-CG-OS 1 0.18 0.0 3.00
DO1-CG-CG-H1 1 0.05 0.0 3.00
DO1-CG-CG-OH 1 -0.10 0.0 -1.00
DO1-CG-CG-OH 1 0.95 0.0 -2.00
DO1-CG-CG-OH 1 0.55 0.0 3.00
DO1-CG-CG-CG 1 0.10 0.0 3.00
DO1-CG-OS-CG 1 0.96 0.0 -3.00
DO1-CG-OS-CG 1 1.38 0.0 -2.00
DO1-CG-OS-CG 1 1.08 0.0 1.00
IMPROPER
NONBON
DO1 1.7210 0.2104
DH1 0.0000 0.0000
DO2 1.2870 0.0157
DH2 0.0000 0.0000
3) leaprc
source leaprc.GLYCAM_06
mol = loadMol2 lam0init.mol2
addatomtypes {
{ "DO1" "O" "sp3" }
{ "DH1" "H" "sp3" }
{ "DO2" "O" "sp3" }
{ "DH2" "H" "sp3" }
}
mol = sequence { mol }
loadamberparams frcmod0
check mol
saveamberparm mol qqqq.top qqqq.crd
quit
4) Error message:
-I: Adding /software/gilgal/amber11/dat/leap/prep to search path.
-I: Adding /software/gilgal/amber11/dat/leap/lib to search path.
-I: Adding /software/gilgal/amber11/dat/leap/parm to search path.
-I: Adding /software/gilgal/amber11/dat/leap/cmd to search path.
Welcome to LEaP!
Sourcing leaprc: ./leaprc
----- Source: /software/gilgal/amber11/dat/leap/cmd/leaprc.GLYCAM_06
----- Source of /software/gilgal/amber11/dat/leap/cmd/leaprc.GLYCAM_06 done
Loading parameters: /software/gilgal/amber11/dat/leap/parm/Glycam_06g.dat
Reading title:
GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
Loading Prep file: /software/gilgal/amber11/dat/leap/prep/GLYCAM_06.prep
Loading library: /software/gilgal/amber11/dat/leap/lib/GLYCAM_amino_06.lib
Loading library: /software/gilgal/amber11/dat/leap/lib/GLYCAM_aminoct_06.lib
Loading library: /software/gilgal/amber11/dat/leap/lib/GLYCAM_aminont_06.lib
Loading library: /software/gilgal/amber11/dat/leap/lib/solvents.lib
Loading Mol2 file: ./lam0init.mol2
Reading MOLECULE named ROH
addAtomTypes: type DO1 - max length is 2
addAtomTypes: type DH1 - max length is 2
addAtomTypes: type DO2 - max length is 2
addAtomTypes: type DH2 - max length is 2
Loading parameters: ./frcmod0
Reading force field modification type file (frcmod)
Reading title:
Glucose parameters for lambda = 0.000000
Checking 'mol'....
Checking parameters for unit 'mol'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
** No torsion terms for OS-CG-DO2-DH2
** No torsion terms for CG-CG-DO2-DH2
** No torsion terms for DO2-CG-CG-H1
** No torsion terms for DO2-CG-CG-OH
** No torsion terms for DO2-CG-CG-CG
** No torsion terms for DO2-CG-OS-CG
** No torsion terms for DO1-CG-DO2-DH2
** No torsion terms for DO1-CG-CG-H1
** No torsion terms for DO1-CG-CG-OH
** No torsion terms for DO1-CG-CG-CG
** No torsion terms for DO1-CG-OS-CG
** No torsion terms for DH1-DO1-CG-DO2
** No torsion terms for DH1-DO1-CG-CG
** No torsion terms for DH1-DO1-CG-OS
Building improper torsion parameters.
total 0 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
Quit
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Received on Fri Apr 13 2012 - 10:30:04 PDT
