Looks to me as if leap didn't like your atom types:
addAtomTypes: type DO1 - max length is 2
I think that is the main thing Leap didn't like.
BTW, if you put "GLYCAM" in the subject line, I might be the only one
to read the email. If your problem really isn't with glycam (and
doesn't appear to be in this case), you will get better results if
your subject heading specifies what the problem is. In this case, you
are having trouble specifying dummy atoms. I haven't done anything
with dummy atoms since Amber 8. So, I might not be your best bet for
help.
One other possibility: It certainly would not hurt to load the
parameters before loading the molecule.
> loadamberparams frcmod0
Back when I did work with dummy atoms, I recall using atomic numbers
to replace element letters. For example, C becomes 6, O becomes 8.
Then, I could easily tell how the dummy atoms mapped without
increasing the character count.
I know some folks use type names that are longer than two characters.
But, I don't know how they made it work.
:-) Lachele
On Fri, Apr 13, 2012 at 1:25 PM, Kepa K. Burusco <kekoburgo.yahoo.es> wrote:
> 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
> _______________________________________________
> 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 Fri Apr 13 2012 - 11:00:02 PDT
