7mjo

gistfile1.txt

Running ANTECHAMBER for residue HIS+HIS
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmpkkmik_9i/ante.in.mol2 -fi mol2 -o /tmp/tmpkkmik_9i/ante.out.mol2 -fo mol2 -c bcc -nc -6 -j 5 -s 2 -dr n
(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


(HIS+HIS) Welcome to antechamber 20.0: molecular input file processor.
(HIS+HIS) `Welcome to antechamber 20.0: molecular input file processor.`  

(HIS+HIS) `Welcome to antechamber 20.0: molecular input file processor.`


(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


(HIS+HIS) Info: Finished reading file (/tmp/tmpkkmik_9i/ante.in.mol2); atoms read (26), bonds read (25).
(HIS+HIS) `Info: Finished reading file (/tmp/tmpkkmik_9i/ante.in.mol2); atoms
read (26), bonds read (25).`  

(HIS+HIS) `Info: Finished reading file (/tmp/tmpkkmik_9i/ante.in.mol2); atoms
read (26), bonds read (25).`


(HIS+HIS) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(HIS+HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  

(HIS+HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`


(HIS+HIS) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  

(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`


(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


(HIS+HIS) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  

(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`


(HIS+HIS) Info: Total number of electrons: 116; net charge: -6
(HIS+HIS) `Info: Total number of electrons: 116; net charge: -6`  

(HIS+HIS) `Info: Total number of electrons: 116; net charge: -6`


(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


(HIS+HIS) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  

(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`


(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


(HIS+HIS) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1
(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  

(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`


(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


(HIS+HIS) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  

(HIS+HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`


(HIS+HIS) 
(HIS+HIS) ``  

(HIS+HIS) ``


Reading ANTECHAMBER output for residue HIS+HIS
Assigning charges for residue HIS+HIS
Charges for residue HIS+HIS determined
Charges for residue HIS+HIS determined
Coulombic values for 7mjo.pdb_A SES surface #1.4: minimum, -13.50, mean 2.22, maximum 16.36
Coulombic values for 7mjo.pdb_B SES surface #1.5: minimum, -20.20, mean 1.56, maximum 15.97
Coulombic values for 7mjo.pdb_C SES surface #1.6: minimum, -18.53, mean 2.23, maximum 25.23
Coulombic values for 7mjo.pdb_D SES surface #1.7: minimum, -26.71, mean 0.86, maximum 14.28
Coulombic values for 7mjo.pdb_E SES surface #1.8: minimum, -40.39, mean -4.21, maximum 37.96
Coulombic values for 7mjo.pdb_G SES surface #1.9: minimum, -36.22, mean -3.54, maximum 10.36
Finished computing Coulombic potential
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-coulombic.png width 512 height 512 supersample 3
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-coulombic.glb
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-coulombic.x3d
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-coulombic.stl
Executing: color magenta
Colored 34816 atoms, 6 surfaces, 2981 residues, rings, 35189 bonds, and 1348 pseudobonds
Executing: color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 noValueColor magenta
2981 residues, 6 surfaces, atom kd_hydrophobicity range -4.5 to 4.5
2981 residues, 6 surfaces, atom kd_hydrophobicity range -4.5 to 4.5
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-hydropathy.png width 512 height 512 supersample 3
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-hydropathy.glb
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-hydropathy.x3d
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-hydropathy.stl
Executing: rainbow @ca chains palette marine:goldenrod:firebrick:forest:tangerine:grape
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-bychain.png width 512 height 512 supersample 3
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-bychain.glb
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-bychain.x3d
Executing: save /tmp/6167184b62b143001cd9dc72_6/7mjo-surf-bychain.stl
Executing: exit
Exiting ...