Hi all,
As usual thank you for your suggestions..
By following your tips + *for some reason removing connect lines on the
initial pdb file* everything technically works fine..
*if it could be helpful to someone, here the entire series of command lines
used *
Antonios-MacBook-Air:MKC_MD_erase_connect Antonio$ antechamber -i
MKC_DOCKING_POSE_LYS907_HAA_multiple_project_AMBER_erase_connect.pdb -o
MKC.mol2 -fo mol2 -c bcc -s 2
Welcome to antechamber 17.3: molecular input file processor.
/Users/Antonio/Desktop/amber18/bin/to_be_dispatched/antechamber: Fatal
Error!
Need both input and output files and formats.
Use antechamber -h for command-line syntax.
Antonios-MacBook-Air:MKC_MD_erase_connect Antonio$ antechamber -i
MKC_DOCKING_POSE_LYS907_HAA_multiple_project_AMBER_erase_connect.pdb -fi
pdb -o MKC.mol2 -fo mol2 -c bcc -s 2
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Running: /Users/Antonio/Desktop/amber18/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /Users/Antonio/Desktop/amber18/bin/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 178; net charge: 0
Running: /Users/Antonio/Desktop/amber18/bin/sqm -O -i sqm.in -o sqm.out
Running: /Users/Antonio/Desktop/amber18/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/Antonio/Desktop/amber18/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /Users/Antonio/Desktop/amber18/bin/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
Antonios-MacBook-Air:MKC_MD_erase_connect Antonio$ vi sqm.out
Antonios-MacBook-Air:MKC_MD_erase_connect Antonio$ parmchk2 -i MKC.mol2 -f
mol2 -o sustiva.frcmod
Antonios-MacBook-Air:MKC_MD_erase_connect Antonio$ vi sustiva.frcmod
Antonios-MacBook-Air:MKC_MD_erase_connect Antonio$ tleap -f leaprc.ff14SB
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/prep to search path.
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/lib to search path.
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/parm to search path.
-I: Adding /Users/Antonio/Desktop/amber18/dat/leap/cmd to search path.
-f: Source leaprc.ff14SB.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.ff14SB
Log file: ./leap.log
Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters:
/Users/Antonio/Desktop/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/amino12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/aminoct12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/aminont12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/nucleic12.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/atomic_ions.lib
Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> 31J = loadmol2 MKC.mol2
Loading Mol2 file: ./MKC.mol2
Reading MOLECULE named 31J
> list
31J A A3 A5 ACE AG AL ALA
AN ARG ASH ASN ASP Ag BA BR
Be C C3 C5 CA CALA CARG CASN
CASP CCYS CCYX CD CE CGLN CGLU CGLY
CHCL3BOX CHID CHIE CHIP CHIS CHYP CILE CL
CLEU CLYS CMET CN CO CPHE CPRO CR
CS CSER CTHR CTRP CTYR CU CU1 CVAL
CYM CYS CYX Ce Cl- Cr DA DA3
DA5 DAN DC DC3 DC4 DC5 DCN DG
DG3 DG5 DGN DT DT3 DT5 DTN Dy
EU EU3 Er F FB3 FB3BOX FB4
FB4BOX
FE FE2 G G3 G5 GD3 GLH GLN
GLU GLY GN H3O+ HE+ HG HID HIE
HIP HIS HOH HYP HZ+ Hf ILE IN
IOD K K+ LA LEU LI LU LYN
LYS MEOHBOX MET MG MN NA NALA NARG
NASN NASP NCYS NCYX NGLN NGLU NGLY NH4
NHE NHID NHIE NHIP NHIS NI NILE NLEU
NLYS NMABOX NME NMET NPHE NPRO NSER NTHR
NTRP NTYR NVAL Na+ Nd OHE OP3 OPC
OPC3BOX OPCBOX PB PD PHE PL3 POL3BOX PR
PRO PT Pu QSPCFWBOX RB Ra S2P SER
SM SPC SPCBOX SPCFWBOX SPF SPG SR Sm
Sn T2P T4E TB THR TIP3PBOX TIP3PFBOX
TIP4PBOX
TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5 TPF TRP
TYR Th Tl Tm U U3 U4+ U5
UN V2+ VAL WAT Y YB2 ZN Zr
frcmod14SBgaff parm10
> check 31J
Checking '31J'....
Checking parameters for unit '31J'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> loadamberparams sustiva.frcmod
Loading parameters: ./sustiva.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> check 31J
Checking '31J'....
Checking parameters for unit '31J'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveoff 31J 31j.lib
Creating 31j.lib
Building topology.
Building atom parameters.
> saveamberparm 31J MKC.prmtop MKC.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 10 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res
total affected
31J
1
)
(no restraints)
> loadoff 31j.lib
Loading library: ./31j.lib
> complex = loadpdb complex.pdb
Loading PDB file: ./complex.pdb
total atoms in file: 6625
> loadamberparams frcmod.ionsjc_spce
Loading parameters:
/Users/Antonio/Desktop/amber18/dat/leap/parm/frcmod.ionsjc_spce
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and SPC/E water from Joung & Cheatham
JPCB (2008)
> loadamberparams frcmod.spce
Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/frcmod.spce
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for SPC/E water
> solvatebox complex SPCBOX 10.0
Solute vdw bounding box: 87.004 54.346 73.505
Total bounding box for atom centers: 107.004 74.346 93.505
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 110.100 77.495 96.476 angstroms.
Volume: 823155.024 A^3
Total mass 417640.532 amu, Density 0.843 g/cc
Added 20554 residues.
> charge mol
Error: charge: Argument #1 is type String must be of type: [unit molecule
residue atom list]
usage: charge <object>
> charge complex
Total unperturbed charge: -0.001000
Total perturbed charge: -0.001000
> saveamberparm complex complex.prmtop complex.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1379 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res
total affected
31J
1
WAT
20554
)
(no restraints)
> quit
Quit
Exiting LEaP: Errors = 4; Warnings = 0; Notes = 0.
On Tue, Aug 28, 2018 at 11:36 PM David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Aug 28, 2018, Antonio Amber Carlesso wrote:
> >
> > I am trying to correctly prepare a protein with a ligand.
> >
> > > loadMol2 MKC.mol2
>
> Above is the wrong syntax: it should be "31J = loadMol2 MKC.mol2"
> (assuming that, confusingly, the information for unit 31J is actually in
> the file names MKC.mol2).
>
> >
> > Loading Mol2 file: ./MKC.mol2
> > Reading MOLECULE named 31J
>
> If you type "list" after this, I'm guessing you will see that there is
> no unit named 31J in the list of available units
>
> > Creating new UNIT for residue: 31J sequence: 966
> > Created a new atom named: C21 within residue: .R<31J 966>
>
> Above is consistent with the problem noted above.
>
> This is an all-to-easy mistake to make. Maybe Scott (our resident tleap
> fixer) can think about making the syntax of loadMol2 more like that of
> loadOff. Until then, try modifying your script.
>
> ...good luck....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Aug 29 2018 - 03:00:01 PDT
