Hi,
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
See the full output attached.
I tried to use parmchk2 to create frcmod files but get a Segmentation fault after warnings of this kind:
Warning: Atom type (C.ar) 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 (C.ar); set to 0.0.
It is recommended to add the new atom type (C.ar) to PARMCHK.DAT.
Warning: Atom type (C.3) 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 (C.3); set to 0.0.
It is recommended to add the new atom type (C.3) to PARMCHK.DAT.
Warning: Atom type (C.2) is not in PARMCHK.DAT; using default values
for improper_flag [0], group_id [0], and equivalent_flag [0].
I am little stuck here.
cheers
Martin
Welcome to LEaP!
(no leaprc in search path)
>
> DMS=loadmol2 DMS_ideal.mol2
Loading Mol2 file: ./DMS_ideal.mol2
Reading MOLECULE named /tmp/8RFSRM8
> 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>
total atoms in file: 5021
Leap added 677 missing atoms according to residue templates:
1 Heavy
676 H / lone pairs
> solvateoct foo TIP3PBOX 10.0
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
(using default radius 1.500000 for O01)
(using default radius 1.500000 for N05)
(using default radius 1.500000 for C19)
(using default radius 1.500000 for C18)
(using default radius 1.500000 for C16)
(using default radius 1.500000 for C14)
(using default radius 1.500000 for C12)
(using default radius 1.500000 for C11)
(using default radius 1.500000 for C09)
(using default radius 1.500000 for C08)
(using default radius 1.500000 for C07)
(using default radius 1.500000 for C06)
(using default radius 1.500000 for C03)
(using default radius 1.500000 for C02)
(using default radius 1.500000 for C20)
(using default radius 1.500000 for C17)
(using default radius 1.500000 for C15)
(using default radius 1.500000 for C13)
(using default radius 1.500000 for C10)
Scaling up box by a factor of 1.180403 to meet diagonal cut criterion
Solute vdw bounding box: 41.946 82.892 50.767
Total bounding box for atom centers: 106.500 106.500 106.500
(box expansion for 'iso' is 132.6%)
Solvent unit box: 18.774 18.774 18.774
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O)
(using default radius 1.500000 for S)
(using default radius 1.500000 for O01)
(using default radius 1.500000 for N05)
(using default radius 1.500000 for C19)
(using default radius 1.500000 for C18)
(using default radius 1.500000 for C16)
(using default radius 1.500000 for C14)
(using default radius 1.500000 for C12)
(using default radius 1.500000 for C11)
(using default radius 1.500000 for C09)
(using default radius 1.500000 for C08)
(using default radius 1.500000 for C07)
(using default radius 1.500000 for C06)
(using default radius 1.500000 for C03)
(using default radius 1.500000 for C02)
(using default radius 1.500000 for C20)
(using default radius 1.500000 for C17)
(using default radius 1.500000 for C15)
(using default radius 1.500000 for C13)
(using default radius 1.500000 for C10)
Volume: 621150.196 A^3 (oct)
Mass > 339951.680 amu, Density > 0.909 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 16680 residues.
> saveamberparm foo WT.prmtop WT.inpcrd
lapwing.cryst.bbk.ac.uk> tleap
-I: Adding /s/amber/amber18/CentOS7/amber18/dat/leap/prep to search path.
-I: Adding /s/amber/amber18/CentOS7/amber18/dat/leap/lib to search path.
-I: Adding /s/amber/amber18/CentOS7/amber18/dat/leap/parm to search path.
-I: Adding /s/amber/amber18/CentOS7/amber18/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> DMS=loadmol2 DMS_ideal.mol2
Loading Mol2 file: ./DMS_ideal.mol2
Reading MOLECULE named /tmp/8RFSRM8
> 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>
total atoms in file: 5021
Leap added 677 missing atoms according to residue templates:
1 Heavy
676 H / lone pairs
> check foo
Checking 'foo'....
Warning: The unperturbed charge of the unit (-3.998900) is not zero.
Warning: Close contact of 1.453019 angstroms between .R<NSER 1>.A<H3 4> and .R<NSER 1>.A<H2 3>
Warning: Close contact of 1.452949 angstroms between .R<NSER 1>.A<H3 4> and .R<NSER 1>.A<H1 2>
Warning: Close contact of 1.453564 angstroms between .R<NSER 1>.A<H2 3> and .R<NSER 1>.A<H1 2>
Warning: Close contact of 1.435893 angstroms between .R<PHE 3>.A<H 2> and .R<WAT 319>.A<H1 2>
Warning: Close contact of 1.488945 angstroms between .R<ARG 4>.A<HH22 22> and .R<ARG 4>.A<HH21 21>
Warning: Close contact of 1.489202 angstroms between .R<ARG 4>.A<HH12 19> and .R<ARG 4>.A<HH11 18>
Warning: Close contact of 1.452944 angstroms between .R<LYS 5>.A<HZ3 20> and .R<LYS 5>.A<HZ2 19>
Warning: Close contact of 1.453004 angstroms between .R<LYS 5>.A<HZ3 20> and .R<LYS 5>.A<HZ1 18>
Warning: Close contact of 1.349248 angstroms between .R<LYS 5>.A<HZ3 20> and .R<WAT 347>.A<H2 3>
Warning: Close contact of 1.452750 angstroms between .R<LYS 5>.A<HZ2 19> and .R<LYS 5>.A<HZ1 18>
Warning: Close contact of 1.461095 angstroms between .R<LYS 5>.A<H 2> and .R<WAT 320>.A<H1 2>
Warning: Close contact of 1.453578 angstroms between .R<LYS 12>.A<HZ3 20> and .R<LYS 12>.A<HZ2 19>
Warning: Close contact of 1.453902 angstroms between .R<LYS 12>.A<HZ3 20> and .R<LYS 12>.A<HZ1 18>
Warning: Close contact of 1.453819 angstroms between .R<LYS 12>.A<HZ2 19> and .R<LYS 12>.A<HZ1 18>
Warning: Close contact of 1.489564 angstroms between .R<GLN 19>.A<HE22 15> and .R<GLN 19>.A<HE21 14>
Warning: Close contact of 1.016585 angstroms between .R<GLY 23>.A<H 2> and .R<WAT 330>.A<H2 3>
Warning: Close contact of 1.488859 angstroms between .R<ASN 28>.A<HD22 12> and .R<ASN 28>.A<HD21 11>
Warning: Close contact of 1.387099 angstroms between .R<TYR 37>.A<HH 15> and .R<WAT 384>.A<H2 3>
Warning: Close contact of 1.489755 angstroms between .R<ARG 40>.A<HH22 22> and .R<ARG 40>.A<HH21 21>
Warning: Close contact of 1.489473 angstroms between .R<ARG 40>.A<HH12 19> and .R<ARG 40>.A<HH11 18>
Warning: Close contact of 1.490143 angstroms between .R<ASN 51>.A<HD22 12> and .R<ASN 51>.A<HD21 11>
Warning: Close contact of 1.489659 angstroms between .R<ASN 53>.A<HD22 12> and .R<ASN 53>.A<HD21 11>
Warning: Close contact of 1.489336 angstroms between .R<ARG 60>.A<HH22 22> and .R<ARG 60>.A<HH21 21>
Warning: Close contact of 1.489695 angstroms between .R<ARG 60>.A<HH12 19> and .R<ARG 60>.A<HH11 18>
Warning: Close contact of 1.452970 angstroms between .R<LYS 61>.A<HZ3 20> and .R<LYS 61>.A<HZ2 19>
Warning: Close contact of 1.453499 angstroms between .R<LYS 61>.A<HZ3 20> and .R<LYS 61>.A<HZ1 18>
Warning: Close contact of 1.453260 angstroms between .R<LYS 61>.A<HZ2 19> and .R<LYS 61>.A<HZ1 18>
Warning: Close contact of 1.386834 angstroms between .R<SER 62>.A<HG 9> and .R<WAT 378>.A<H1 2>
Warning: Close contact of 1.488943 angstroms between .R<ASN 63>.A<HD22 12> and .R<ASN 63>.A<HD21 11>
Warning: Close contact of 1.400804 angstroms between .R<ASN 63>.A<HD22 12> and .R<WAT 477>.A<H2 3>
Warning: Close contact of 1.394987 angstroms between .R<HID 64>.A<H 2> and .R<WAT 338>.A<H2 3>
Warning: Close contact of 1.490080 angstroms between .R<ASN 65>.A<HD22 12> and .R<ASN 65>.A<HD21 11>
Warning: Close contact of 1.211690 angstroms between .R<VAL 68>.A<H 2> and .R<WAT 435>.A<H2 3>
Warning: Close contact of 1.489279 angstroms between .R<GLN 69>.A<HE22 15> and .R<GLN 69>.A<HE21 14>
Warning: Close contact of 1.489331 angstroms between .R<ASN 72>.A<HD22 12> and .R<ASN 72>.A<HD21 11>
Warning: Close contact of 1.489791 angstroms between .R<GLN 74>.A<HE22 15> and .R<GLN 74>.A<HE21 14>
Warning: Close contact of 1.490130 angstroms between .R<ARG 76>.A<HH22 22> and .R<ARG 76>.A<HH21 21>
Warning: Close contact of 1.488615 angstroms between .R<ARG 76>.A<HH12 19> and .R<ARG 76>.A<HH11 18>
Warning: Close contact of 1.489444 angstroms between .R<GLN 83>.A<HE22 15> and .R<GLN 83>.A<HE21 14>
Warning: Close contact of 1.489460 angstroms between .R<ASN 84>.A<HD22 12> and .R<ASN 84>.A<HD21 11>
Warning: Close contact of 1.452789 angstroms between .R<LYS 88>.A<HZ3 20> and .R<LYS 88>.A<HZ2 19>
Warning: Close contact of 1.454168 angstroms between .R<LYS 88>.A<HZ3 20> and .R<LYS 88>.A<HZ1 18>
Warning: Close contact of 1.453104 angstroms between .R<LYS 88>.A<HZ2 19> and .R<LYS 88>.A<HZ1 18>
Warning: Close contact of 1.453193 angstroms between .R<LYS 90>.A<HZ3 20> and .R<LYS 90>.A<HZ2 19>
Warning: Close contact of 1.452438 angstroms between .R<LYS 90>.A<HZ3 20> and .R<LYS 90>.A<HZ1 18>
Warning: Close contact of 1.453102 angstroms between .R<LYS 90>.A<HZ2 19> and .R<LYS 90>.A<HZ1 18>
Warning: Close contact of 1.142862 angstroms between .R<ALA 94>.A<H 2> and .R<WAT 497>.A<H2 3>
Warning: Close contact of 1.489663 angstroms between .R<ASN 95>.A<HD22 12> and .R<ASN 95>.A<HD21 11>
Warning: Close contact of 1.453253 angstroms between .R<LYS 97>.A<HZ3 20> and .R<LYS 97>.A<HZ2 19>
Warning: Close contact of 1.453122 angstroms between .R<LYS 97>.A<HZ3 20> and .R<LYS 97>.A<HZ1 18>
Warning: Close contact of 1.453847 angstroms between .R<LYS 97>.A<HZ2 19> and .R<LYS 97>.A<HZ1 18>
Warning: Close contact of 1.452972 angstroms between .R<LYS 100>.A<HZ3 20> and .R<LYS 100>.A<HZ2 19>
Warning: Close contact of 1.453190 angstroms between .R<LYS 100>.A<HZ3 20> and .R<LYS 100>.A<HZ1 18>
Warning: Close contact of 1.453317 angstroms between .R<LYS 100>.A<HZ2 19> and .R<LYS 100>.A<HZ1 18>
Warning: Close contact of 1.361343 angstroms between .R<TYR 101>.A<H 2> and .R<WAT 538>.A<H2 3>
Warning: Close contact of 1.453380 angstroms between .R<LYS 102>.A<HZ3 20> and .R<LYS 102>.A<HZ2 19>
Warning: Close contact of 1.453460 angstroms between .R<LYS 102>.A<HZ3 20> and .R<LYS 102>.A<HZ1 18>
Warning: Close contact of 1.452992 angstroms between .R<LYS 102>.A<HZ2 19> and .R<LYS 102>.A<HZ1 18>
Warning: Close contact of 1.441416 angstroms between .R<PHE 103>.A<H 2> and .R<WAT 474>.A<H2 3>
Warning: Close contact of 1.489642 angstroms between .R<ARG 105>.A<HH22 22> and .R<ARG 105>.A<HH21 21>
Warning: Close contact of 1.489683 angstroms between .R<ARG 105>.A<HH12 19> and .R<ARG 105>.A<HH11 18>
Warning: Close contact of 1.489867 angstroms between .R<GLN 107>.A<HE22 15> and .R<GLN 107>.A<HE21 14>
Warning: Close contact of 1.489796 angstroms between .R<GLN 110>.A<HE22 15> and .R<GLN 110>.A<HE21 14>
Warning: Close contact of 1.328518 angstroms between .R<GLN 110>.A<HG3 10> and .R<WAT 457>.A<H2 3>
Warning: Close contact of 1.489573 angstroms between .R<ASN 119>.A<HD22 12> and .R<ASN 119>.A<HD21 11>
Warning: Close contact of 1.489226 angstroms between .R<GLN 127>.A<HE22 15> and .R<GLN 127>.A<HE21 14>
Warning: Close contact of 1.489880 angstroms between .R<ARG 131>.A<HH22 22> and .R<ARG 131>.A<HH21 21>
Warning: Close contact of 1.489611 angstroms between .R<ARG 131>.A<HH12 19> and .R<ARG 131>.A<HH11 18>
Warning: Close contact of 1.489051 angstroms between .R<ASN 133>.A<HD22 12> and .R<ASN 133>.A<HD21 11>
Warning: Close contact of 1.390911 angstroms between .R<ASN 133>.A<HD21 11> and .R<WAT 375>.A<H1 2>
Warning: Close contact of 1.452803 angstroms between .R<LYS 137>.A<HZ3 20> and .R<LYS 137>.A<HZ2 19>
Warning: Close contact of 1.452741 angstroms between .R<LYS 137>.A<HZ3 20> and .R<LYS 137>.A<HZ1 18>
Warning: Close contact of 1.453170 angstroms between .R<LYS 137>.A<HZ2 19> and .R<LYS 137>.A<HZ1 18>
Warning: Close contact of 1.490322 angstroms between .R<ASN 142>.A<HD22 12> and .R<ASN 142>.A<HD21 11>
Warning: Close contact of 0.725876 angstroms between .R<CYS 145>.A<SG 8> and .R<T8A 308>.A<H031 26>
Warning: Close contact of 1.391179 angstroms between .R<VAL 148>.A<H 2> and .R<WAT 353>.A<H1 2>
Warning: Close contact of 1.489482 angstroms between .R<ASN 151>.A<HD22 12> and .R<ASN 151>.A<HD21 11>
Warning: Close contact of 1.210352 angstroms between .R<ASN 151>.A<HD22 12> and .R<WAT 423>.A<H2 3>
Warning: Close contact of 1.457294 angstroms between .R<GLU 166>.A<OE1 12> and .R<WAT 310>.A<H1 2>
Warning: Close contact of 1.489438 angstroms between .R<ASN 180>.A<HD22 12> and .R<ASN 180>.A<HD21 11>
Warning: Close contact of 1.490503 angstroms between .R<ARG 188>.A<HH22 22> and .R<ARG 188>.A<HH21 21>
Warning: Close contact of 1.489919 angstroms between .R<ARG 188>.A<HH12 19> and .R<ARG 188>.A<HH11 18>
Warning: Close contact of 1.489507 angstroms between .R<GLN 189>.A<HE22 15> and .R<GLN 189>.A<HE21 14>
Warning: Close contact of 1.489589 angstroms between .R<GLN 192>.A<HE22 15> and .R<GLN 192>.A<HE21 14>
Warning: Close contact of 1.099788 angstroms between .R<ALA 194>.A<H 2> and .R<WAT 422>.A<H1 2>
Warning: Close contact of 0.922629 angstroms between .R<GLY 195>.A<H 2> and .R<WAT 420>.A<H2 3>
Warning: Close contact of 1.489616 angstroms between .R<ASN 203>.A<HD22 12> and .R<ASN 203>.A<HD21 11>
Warning: Close contact of 1.436230 angstroms between .R<TRP 207>.A<HE1 12> and .R<WAT 475>.A<H1 2>
Warning: Close contact of 1.489143 angstroms between .R<ASN 214>.A<HD22 12> and .R<ASN 214>.A<HD21 11>
Warning: Close contact of 1.489803 angstroms between .R<ARG 217>.A<HH22 22> and .R<ARG 217>.A<HH21 21>
Warning: Close contact of 1.352161 angstroms between .R<ARG 217>.A<HH22 22> and .R<WAT 314>.A<H2 3>
Warning: Close contact of 1.489696 angstroms between .R<ARG 217>.A<HH12 19> and .R<ARG 217>.A<HH11 18>
Warning: Close contact of 1.123736 angstroms between .R<ARG 217>.A<H 2> and .R<WAT 443>.A<H1 2>
Warning: Close contact of 1.490156 angstroms between .R<ASN 221>.A<HD22 12> and .R<ASN 221>.A<HD21 11>
Warning: Close contact of 1.488931 angstroms between .R<ARG 222>.A<HH22 22> and .R<ARG 222>.A<HH21 21>
Warning: Close contact of 1.489097 angstroms between .R<ARG 222>.A<HH12 19> and .R<ARG 222>.A<HH11 18>
Warning: Close contact of 1.489980 angstroms between .R<ASN 228>.A<HD22 12> and .R<ASN 228>.A<HD21 11>
Warning: Close contact of 1.489446 angstroms between .R<ASN 231>.A<HD22 12> and .R<ASN 231>.A<HD21 11>
Warning: Close contact of 1.453499 angstroms between .R<LYS 236>.A<HZ3 20> and .R<LYS 236>.A<HZ2 19>
Warning: Close contact of 1.453255 angstroms between .R<LYS 236>.A<HZ3 20> and .R<LYS 236>.A<HZ1 18>
Warning: Close contact of 1.453684 angstroms between .R<LYS 236>.A<HZ2 19> and .R<LYS 236>.A<HZ1 18>
Warning: Close contact of 1.474121 angstroms between .R<LYS 236>.A<HZ1 18> and .R<WAT 327>.A<H1 2>
Warning: Close contact of 1.223087 angstroms between .R<TYR 237>.A<HH 15> and .R<WAT 379>.A<H1 2>
Warning: Close contact of 1.490222 angstroms between .R<ASN 238>.A<HD22 12> and .R<ASN 238>.A<HD21 11>
Warning: Close contact of 1.419337 angstroms between .R<TYR 239>.A<HH 15> and .R<WAT 349>.A<H1 2>
Warning: Close contact of 1.489241 angstroms between .R<GLN 244>.A<HE22 15> and .R<GLN 244>.A<HE21 14>
Warning: Close contact of 1.461661 angstroms between .R<HIE 246>.A<HE2 13> and .R<WAT 341>.A<H2 3>
Warning: Close contact of 1.490066 angstroms between .R<GLN 256>.A<HE22 15> and .R<GLN 256>.A<HE21 14>
Warning: Close contact of 1.399500 angstroms between .R<GLN 256>.A<HE21 14> and .R<WAT 454>.A<H1 2>
Warning: Close contact of 1.453124 angstroms between .R<LYS 269>.A<HZ3 20> and .R<LYS 269>.A<HZ2 19>
Warning: Close contact of 1.453721 angstroms between .R<LYS 269>.A<HZ3 20> and .R<LYS 269>.A<HZ1 18>
Warning: Close contact of 1.453476 angstroms between .R<LYS 269>.A<HZ2 19> and .R<LYS 269>.A<HZ1 18>
Warning: Close contact of 1.490219 angstroms between .R<GLN 273>.A<HE22 15> and .R<GLN 273>.A<HE21 14>
Warning: Close contact of 1.489229 angstroms between .R<ASN 274>.A<HD22 12> and .R<ASN 274>.A<HD21 11>
Warning: Close contact of 1.489629 angstroms between .R<ASN 277>.A<HD22 12> and .R<ASN 277>.A<HD21 11>
Warning: Close contact of 1.488912 angstroms between .R<ARG 279>.A<HH22 22> and .R<ARG 279>.A<HH21 21>
Warning: Close contact of 1.389131 angstroms between .R<ARG 279>.A<HH21 21> and .R<WAT 368>.A<H1 2>
Warning: Close contact of 1.489893 angstroms between .R<ARG 279>.A<HH12 19> and .R<ARG 279>.A<HH11 18>
Warning: Close contact of 1.301174 angstroms between .R<THR 280>.A<HG1 12> and .R<WAT 468>.A<H2 3>
Warning: Close contact of 1.463049 angstroms between .R<GLU 288>.A<OE1 12> and .R<WAT 309>.A<H2 3>
Warning: Close contact of 1.135604 angstroms between .R<THR 292>.A<HG1 12> and .R<WAT 343>.A<H2 3>
Warning: Close contact of 1.198840 angstroms between .R<PRO 293>.A<HD2 3> and .R<WAT 464>.A<H2 3>
Warning: Close contact of 1.489300 angstroms between .R<ARG 298>.A<HH22 22> and .R<ARG 298>.A<HH21 21>
Warning: Close contact of 1.489717 angstroms between .R<ARG 298>.A<HH12 19> and .R<ARG 298>.A<HH11 18>
Warning: Close contact of 1.489793 angstroms between .R<GLN 299>.A<HE22 15> and .R<GLN 299>.A<HE21 14>
Warning: Close contact of 1.356736 angstroms between .R<WAT 317>.A<H2 3> and .R<WAT 438>.A<H1 2>
Warning: Close contact of 1.317771 angstroms between .R<WAT 318>.A<H1 2> and .R<WAT 548>.A<H2 3>
Warning: Close contact of 1.115688 angstroms between .R<WAT 321>.A<H1 2> and .R<WAT 479>.A<H2 3>
Warning: Close contact of 1.396000 angstroms between .R<WAT 339>.A<H1 2> and .R<WAT 489>.A<H2 3>
Warning: Close contact of 1.416354 angstroms between .R<WAT 367>.A<H1 2> and .R<WAT 626>.A<H2 3>
Warning: Close contact of 1.196564 angstroms between .R<WAT 385>.A<H1 2> and .R<WAT 396>.A<H2 3>
Warning: Close contact of 1.128019 angstroms between .R<WAT 391>.A<H1 2> and .R<WAT 502>.A<H2 3>
Warning: Close contact of 1.177688 angstroms between .R<WAT 421>.A<H1 2> and .R<WAT 576>.A<H2 3>
Warning: Close contact of 1.398593 angstroms between .R<WAT 421>.A<H1 2> and .R<WAT 576>.A<O 1>
Warning: Close contact of 1.332781 angstroms between .R<WAT 422>.A<H2 3> and .R<WAT 564>.A<O 1>
Warning: Close contact of 1.383272 angstroms between .R<WAT 434>.A<H1 2> and .R<WAT 549>.A<O 1>
Warning: Close contact of 1.138574 angstroms between .R<WAT 459>.A<H1 2> and .R<WAT 481>.A<H2 3>
Warning: Close contact of 1.316806 angstroms between .R<WAT 460>.A<H2 3> and .R<WAT 612>.A<H1 2>
Warning: Close contact of 1.438787 angstroms between .R<WAT 463>.A<H1 2> and .R<WAT 490>.A<H2 3>
Warning: Close contact of 1.016258 angstroms between .R<WAT 466>.A<H1 2> and .R<WAT 633>.A<H2 3>
Warning: Close contact of 1.430220 angstroms between .R<WAT 539>.A<H1 2> and .R<WAT 571>.A<O 1>
Checking parameters for unit 'foo'.
Checking for bond parameters.
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: s4 - o
Error: Could not find bond parameter for: s4 - c3
Error: Could not find bond parameter for: s4 - c3
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: s4 - o
Error: Could not find bond parameter for: s4 - c3
Error: Could not find bond parameter for: s4 - c3
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: s4 - o
Error: Could not find bond parameter for: s4 - c3
Error: Could not find bond parameter for: s4 - c3
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: c3 - ca
Error: Could not find bond parameter for: c3 - n
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - hc
Error: Could not find bond parameter for: c3 - hc
Error: Could not find bond parameter for: c3 - hc
Error: Could not find bond parameter for: c - c3
Error: Could not find bond parameter for: c - n
Error: Could not find bond parameter for: c - o
Error: Could not find bond parameter for: c3 - n
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: c3 - h1
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ha
Error: Could not find bond parameter for: c3 - c3
Error: Could not find bond parameter for: c3 - ca
Error: Could not find bond parameter for: c3 - ca
Error: Could not find bond parameter for: c3 - hc
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ca
Error: Could not find bond parameter for: ca - ha
Checking for angle parameters.
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: c3 - s4 - c3
Error: Could not find angle parameter: o - s4 - c3
Error: Could not find angle parameter: o - s4 - c3
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: c3 - s4 - c3
Error: Could not find angle parameter: o - s4 - c3
Error: Could not find angle parameter: o - s4 - c3
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: c3 - s4 - c3
Error: Could not find angle parameter: o - s4 - c3
Error: Could not find angle parameter: o - s4 - c3
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: s4 - c3 - h1
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: hc - c3 - hc
Error: Could not find angle parameter: hc - c3 - hc
Error: Could not find angle parameter: hc - c3 - hc
Error: Could not find angle parameter: h1 - c3 - h1
Error: Could not find angle parameter: n - c3 - h1
Error: Could not find angle parameter: n - c3 - h1
Error: Could not find angle parameter: n - c - o
Error: Could not find angle parameter: n - c3 - h1
Error: Could not find angle parameter: n - c3 - h1
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - c3 - hc
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - c3 - ca
Error: Could not find angle parameter: ca - c3 - hc
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - c3 - n
Error: Could not find angle parameter: ca - c3 - h1
Error: Could not find angle parameter: ca - c3 - h1
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: c3 - ca - ca
Error: Could not find angle parameter: c3 - ca - ca
Error: Could not find angle parameter: c3 - c - n
Error: Could not find angle parameter: c3 - c - o
Error: Could not find angle parameter: c - c3 - hc
Error: Could not find angle parameter: c - c3 - hc
Error: Could not find angle parameter: c - c3 - hc
Error: Could not find angle parameter: c - n - c3
Error: Could not find angle parameter: c3 - c3 - ca
Error: Could not find angle parameter: c3 - c3 - ca
Error: Could not find angle parameter: c3 - c3 - hc
Error: Could not find angle parameter: c3 - n - c
Error: Could not find angle parameter: c3 - n - c3
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: c3 - c3 - n
Error: Could not find angle parameter: c3 - c3 - h1
Error: Could not find angle parameter: c3 - c3 - h1
Error: Could not find angle parameter: c3 - ca - ca
Error: Could not find angle parameter: c3 - ca - ca
Error: Could not find angle parameter: c3 - ca - ca
Error: Could not find angle parameter: c3 - ca - ca
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Error: Could not find angle parameter: ca - ca - ca
Error: Could not find angle parameter: ca - ca - ha
Warning: There are missing parameters.
check: Warnings: 142
Unit is OK.
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Received on Sun Mar 29 2020 - 06:00:07 PDT
