Hi Dac,
thanks for the help.
On Sun, Mar 29, 2020, Rosellen, Martin wrote:
I want to solvate a structure (5rft) containing small ligands. I download
the pdbs of the ligands and convert them into a mol2 file. In tleap
checking the loaded pdb I get a lot of errors of this type:
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
It looks like you failed to load gaff2.dat, which contains the
parameters you need.
I tried to use parmchk2 to create frcmod files but get a Segmentation fault after warnings of this kind:
Warning: Atom type (C.ar<http://C.ar>) is not in PARMCHK.DAT; using default values
for improper_flag [0], group_id [0], and equivalent_flag [0].
Looks like you created your mol2 with some other program(?) that is
using Sybyl atom types. parmchk2 can only handle Amber or gaff(2) atom
types. You should use antechamber to make the mol2 files (with gaff2
atom types).
I created the mol2 file with antechamber and it looks like this now:
.<TRIPOS>MOLECULE
DMS
10 10 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 S 0.1540 -0.3710 0.0000 s6 1 DMS 0.000000
2 O 1.3900 0.3310 0.0010 os 1 DMS 0.000000
3 C1 -0.8640 0.1960 1.3890 c3 1 DMS 0.000000
4 C2 -0.8620 0.1960 -1.3900 c3 1 DMS 0.000000
5 H11 -0.3810 -0.0730 2.3280 h1 1 DMS 0.000000
6 H12 -0.9780 1.2790 1.3370 h1 1 DMS 0.000000
7 H13 -1.8450 -0.2750 1.3360 h1 1 DMS 0.000000
8 H21 -0.3780 -0.0720 -2.3280 h1 1 DMS 0.000000
9 H22 -1.8430 -0.2750 -1.3390 h1 1 DMS 0.000000
10 H23 -0.9770 1.2790 -1.3380 h1 1 DMS 0.000000
.<TRIPOS>BOND
1 1 2 1
2 1 2 1
3 1 3 1
4 1 4 1
5 3 5 1
6 3 6 1
7 3 7 1
8 4 8 1
9 4 9 1
10 4 10 1
.<TRIPOS>SUBSTRUCTURE
1 DMS 1 TEMP 0 **** **** 0 ROOT
However, when I use it in tleap I run into an error:
Welcome to LEaP!
(no leaprc in search path)
> DMS=loadmol2 DMS_ideal.mol2
Loading Mol2 file: ./DMS_ideal.mol2
Reading MOLECULE named DMS
> T8A=loadmol2 T8A_ideal.mol2
Loading Mol2 file: ./T8A_ideal.mol2
Reading MOLECULE named T8A
> source leaprc.water.tip3p
----- Source: /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.water.tip3p
----- Source of /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /s/amber/amber18/CentOS7/amber18/dat/leap/lib/atomic_ions.lib
Loading library: /s/amber/amber18/CentOS7/amber18/dat/leap/lib/solvents.lib
Loading parameters: /s/amber/amber18/CentOS7/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: /s/amber/amber18/CentOS7/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: /s/amber/amber18/CentOS7/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 leaprc.protein.ff14SB
----- Source: /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /s/amber/amber18/CentOS7/amber18/dat/leap/lib/amino12.lib
Loading library: /s/amber/amber18/CentOS7/amber18/dat/leap/lib/aminoct12.lib
Loading library: /s/amber/amber18/CentOS7/amber18/dat/leap/lib/aminont12.lib
> set default PBradii mbondi2
Using H(N)-modified Bondi radii
> foo=loadpdb 5rftH_amb.pdb
Loading PDB file: ./5rftH_amb.pdb
Added missing heavy atom: .R<CTHR 304>.A<OXT 15>
Error: Atom .R<DMS 1>.A<S 1> has force field coordination 4
but only 3 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon (if running interactively).
Error: Atom .R<DMS 1>.A<O 2> has force field coordination 2
but only 1 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon (if running interactively).
/s/amber/amber18/CentOS7/amber18/bin/tleap: line 10: 6200 Segmentation fault (core dumped) $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
....good luck...dac
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Received on Fri Apr 03 2020 - 01:30:02 PDT
