Hello,
I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page:
http://www.probechem.com/products_PRG-A01.html
I used the guide made by Michael Barton and Tyler Luchko at the following link: https://ambermd.org/tutorials/basic/tutorial4b/index.php
At first, I obtained the sdf structure thanks to the PDB Chemical sketch tool and converted into pdb using MOE (I simply did a quick prep and saved as pdb):
HEADER
REMARK 99
REMARK 99 MOE v2022.02 (Chemical Computing Group ULC) Thu Jul 18 15:08:13 2024
HETATM 1 O1 * 0 -16.219 1.636 -1.486 1.00 0.00 O1-
HETATM 2 C2 * 0 -16.359 1.987 0.839 1.00 0.00 C
HETATM 3 C3 * 0 -15.215 1.727 1.387 1.00 0.00 C
HETATM 4 C4 * 0 -14.286 1.316 0.345 1.00 0.00 C
HETATM 5 C5 * 0 -14.732 1.265 -1.013 1.00 0.00 C
HETATM 6 O6 * 0 -18.237 2.364 -0.412 1.00 0.00 O1-
HETATM 7 C7 * 0 -13.868 0.878 -2.019 1.00 0.00 C
HETATM 8 C8 * 0 -12.967 0.968 0.644 1.00 0.00 C
HETATM 9 C9 * 0 -12.095 0.571 -0.368 1.00 0.00 C
HETATM 10 C10 * 0 -12.557 0.538 -1.694 1.00 0.00 C
HETATM 11 O11 * 0 -11.720 0.155 -2.719 1.00 0.00 O
HETATM 12 C12 * 0 -10.666 0.191 -0.042 1.00 0.00 C
HETATM 13 C13 * 0 -10.048 -0.656 -1.169 1.00 0.00 C
HETATM 14 C14 * 0 -10.295 -0.012 -2.565 1.00 0.00 C
HETATM 15 O15 * 0 -8.647 -1.082 -0.914 1.00 0.00 O
HETATM 16 C16 * 0 -7.582 -0.324 -0.570 1.00 0.00 C
HETATM 17 C17 * 0 -3.884 -0.967 0.266 1.00 0.00 C
HETATM 18 C18 * 0 -2.759 -0.142 0.425 1.00 0.00 C
HETATM 19 C19 * 0 -3.711 -2.361 0.368 1.00 0.00 C
HETATM 20 C20 * 0 -2.456 -2.913 0.611 1.00 0.00 C
HETATM 21 C21 * 0 -1.348 -2.080 0.760 1.00 0.00 C
HETATM 22 C22 * 0 -1.503 -0.685 0.667 1.00 0.00 C
HETATM 23 C23 * 0 -17.053 2.034 -0.313 1.00 0.00 C2+
HETATM 24 O24 * 0 -0.472 0.237 0.803 1.00 0.00 O
HETATM 25 C25 * 0 0.938 -0.002 1.045 1.00 0.00 C
HETATM 26 O26 * 0 -0.128 -2.662 0.996 1.00 0.00 O
HETATM 27 O27 * 0 -7.741 0.878 -0.488 1.00 0.00 O
HETATM 28 C28 * 0 -6.328 -1.001 -0.330 1.00 0.00 C
HETATM 29 C29 * 0 -5.180 -0.349 0.009 1.00 0.00 C
HETATM 30 C30 * 0 -9.657 1.367 -2.812 1.00 0.00 C
HETATM 31 C31 * 0 -9.841 -0.960 -3.684 1.00 0.00 C
HETATM 32 H1 * 0 -15.058 1.822 2.431 1.00 0.00 H
HETATM 33 H2 * 0 -14.215 0.846 -3.017 1.00 0.00 H
HETATM 34 H3 * 0 -12.658 1.015 1.655 1.00 0.00 H
HETATM 35 H4 * 0 -10.648 -0.384 0.884 1.00 0.00 H
HETATM 36 H5 * 0 -10.104 1.111 0.115 1.00 0.00 H
HETATM 37 H6 * 0 -10.621 -1.586 -1.176 1.00 0.00 H
HETATM 38 H7 * 0 -2.853 0.911 0.359 1.00 0.00 H
HETATM 39 H8 * 0 -4.540 -3.012 0.267 1.00 0.00 H
HETATM 40 H9 * 0 -2.348 -3.965 0.684 1.00 0.00 H
HETATM 41 H10 * 0 1.472 0.947 1.100 1.00 0.00 H
HETATM 42 H11 * 0 1.369 -0.595 0.238 1.00 0.00 H
HETATM 43 H12 * 0 1.079 -0.533 1.988 1.00 0.00 H
HETATM 44 H13 * 0 -0.168 -3.639 1.036 1.00 0.00 H
HETATM 45 H14 * 0 -6.360 -2.051 -0.440 1.00 0.00 H
HETATM 46 H15 * 0 -5.204 0.711 0.095 1.00 0.00 H
HETATM 47 H16 * 0 -9.951 2.073 -2.035 1.00 0.00 H
HETATM 48 H17 * 0 -10.009 1.765 -3.764 1.00 0.00 H
HETATM 49 H18 * 0 -8.571 1.298 -2.846 1.00 0.00 H
HETATM 50 H19 * 0 -8.762 -1.107 -3.654 1.00 0.00 H
HETATM 51 H20 * 0 -10.117 -0.544 -4.654 1.00 0.00 H
HETATM 52 H21 * 0 -10.340 -1.924 -3.580 1.00 0.00 H
CONECT 1 5 23
CONECT 2 3 3 23
CONECT 3 2 2 4 32
CONECT 4 3 5 5 8
CONECT 5 1 4 4 7
CONECT 6 23
CONECT 7 5 10 10 33
CONECT 8 4 9 9 34
CONECT 9 8 8 10 12
CONECT 10 7 7 9 11
CONECT 11 10 14
CONECT 12 9 13 35 36
CONECT 13 12 14 15 37
CONECT 14 11 13 30 31
CONECT 15 13 16
CONECT 16 15 27 27 28
CONECT 17 18 19 19 29
CONECT 18 17 22 22 38
CONECT 19 17 17 20 39
CONECT 20 19 21 21 40
CONECT 21 20 20 22 26
CONECT 22 18 18 21 24
CONECT 23 1 2 6
CONECT 24 22 25
CONECT 25 24 41 42 43
CONECT 26 21 44
CONECT 27 16 16
CONECT 28 16 29 29 45
CONECT 29 17 28 28 46
CONECT 30 14 47 48 49
CONECT 31 14 50 51 52
CONECT 32 3
CONECT 33 7
CONECT 34 8
CONECT 35 12
CONECT 36 12
CONECT 37 13
CONECT 38 18
CONECT 39 19
CONECT 40 20
CONECT 41 25
CONECT 42 25
CONECT 43 25
CONECT 44 26
CONECT 45 28
CONECT 46 29
CONECT 47 30
CONECT 48 30
CONECT 49 30
CONECT 50 31
CONECT 51 31
CONECT 52 31
END
Then I used the following instructions adapted from the guide:
obabel PRG_A01.pdb -O PRG_A01_h.pdb -h
antechamber -i PRG_A01_h.pdb -fi pdb -o PRG_A01.mol2 -fo mol2 -c bcc -s 2
parmchk2 -i PRG_A01.mol2 -f mol2 -o PRG_A01.frcmod
tleap
source leaprc.protein.ff19SB
source leaprc.gaff
PRG = loadmol2 PRG_A01.mol2
loadamberparams PRG_A01.frcmod
saveoff PRG PRG_A01.lib
saveamberparm PRG PRG_A01.prmtop PRG_A01.rst7
The PRG_A01.frcmod file when opened gives:
"Remark line goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
NONBON"
So I don't know if the line of instruction "parmchk2 -i PRG_A01.mol2 -f mol2 -o PRG_A01.frcmod" did properly its job.
Furthermore this is what each instruction returned.
[marco99@narval2 PRG_A01 preparation]$ obabel PRG_A01.pdb -O PRG_A01_h.pdb -h
[mii] Please select a module to run obabel:
MODULE PARENT(S)
1 openbabel/3.1.1 StdEnv/2023 gcc/12.3
2 openbabel-omp/3.1.1 StdEnv/2023 gcc/12.3
3 openbabel/3.1.1 StdEnv/2020 intel/2020.1.217
4 openbabel-omp/3.1.1 StdEnv/2020 intel/2020.1.217
5 gnina/1.0.1 StdEnv/2020 gcc/9.3.0 cuda/11.0
6 openbabel/3.1.1 StdEnv/2020 gcc/9.3.0
7 openbabel-omp/3.1.1 StdEnv/2020 gcc/9.3.0
Make a selection (1-7, q aborts) [1]: 1
[mii] loading StdEnv/2023 gcc/12.3 openbabel/3.1.1 ...
Lmod is automatically replacing "boost-mpi/1.82.0" with "boost/1.82.0".
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
The following dependent module(s) are not currently loaded: boost-mpi/1.82.0 (required by: amber/22.5-23.5)
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
1 molecule converted
[marco99@narval2 PRG_A01 preparation]$ antechamber -i PRG_A01_h.pdb -fi pdb -o PRG_A01.mol2 -fo mol2 -c bcc -s 2
Welcome to antechamber 22.0: molecular input file processor.
Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb File --
Status: pass
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- 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: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 222; net charge: 0
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/sqm -O -i sqm.in -o sqm.out
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 0, Name: O1).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 1, Name: C2).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 2, Name: C3).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 5, Name: O6).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 5, Name: O6).
Automatically increasing to 15000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 5, Name: O6).
Automatically increasing to 20000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 17, Name: C18).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 17, Name: C18).
Automatically increasing to 15000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 18, Name: C19).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 19, Name: C20).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 20, Name: C21).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 21, Name: C22).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 22, Name: C23).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 23, Name: O24).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 24, Name: C25).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 25, Name: O26).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 31, Name: H1).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 37, Name: H7).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 37, Name: H7).
Automatically increasing to 15000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 38, Name: H8).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 39, Name: H9).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 40, Name: H10).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 41, Name: H11).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 42, Name: H12).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 43, Name: H13).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 52, Name: H).
Automatically increasing to 10000.
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
[marco99@narval2 PRG_A01 preparation]$ ^C
[marco99@narval2 PRG_A01 preparation]$ parmchk2 -i PRG_A01.mol2 -f mol2 -o PRG_A01.frcmod
[marco99@narval2 PRG_A01 preparation]$ tleap
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/prep to search path.
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib to search path.
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm to search path.
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.protein.ff19SB
----- Source: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.protein.ff19SB
----- Source of /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.protein.ff19SB done
Log file: ./leap.log
Loading parameters: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm/parm19.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB
Loading parameters: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm/frcmod.ff19SB
Reading force field modification type file (frcmod)
Reading title:
ff19SB AA-specific backbone CMAPs for protein 07/25/2019
Loading library: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib/amino19.lib
Loading library: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib/aminoct12.lib
Loading library: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib/aminont12.lib
> source leaprc.gaff
----- Source: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.gaff
----- Source of /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> PRG = loadmol2 PRG_A01.mol2
Loading Mol2 file: ./PRG_A01.mol2
Reading MOLECULE named *
> loadamberparams PRG_A01.frcmod
Loading parameters: ./PRG_A01.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> saveoff PRG PRG_A01.lib
Creating PRG_A01.lib
Building topology.
Building atom parameters.
> saveamberparm PRG PRG_A01.prmtop PRG_A01.rst7
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL: In file [/tmp/ebuser/avx2/Amber/22.5-23.5/gofbc-2023a/AmberTools/src/leap/src/leap/unitio.c], line 1955
!FATAL: Message: 1-4: cannot add bond 2 3
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
!
!ABORTING.
The last instruction "saveamberparm PRG PRG_A01.prmtop PRG_A01.rst7" gives the fatal error I'm worried about:
!FATAL ERROR----------------------------------------
!FATAL: In file [/tmp/ebuser/avx2/Amber/22.5-23.5/gofbc-2023a/AmberTools/src/leap/src/leap/unitio.c], line 1955
!FATAL: Message: 1-4: cannot add bond 2 3
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
!
I tried to remove the conects and remarks from the PDB file of the structure (which MOE added), resulting in the same error.
Is there a ways to face this obstacle?
Thank you very much
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