Dear amber users,
I want to do MD simulation of a protein-ligand complex and binding free
energy. My ligand is paclitaxel (taxol) which has complex chemical
structure.
I obtained position and orientation of taxol in the binding site of protein
after docking using autodock.
Dou to the lack of Hydrogen atoms in the taxol structure after docking, I
added Hydrogen atoms using h_add in Pymol.
Unfortunately, Pymol adds two Hydrogen atoms to two Carbon atoms that
should not have Hydrogen (before adding Hydrogen, the valence of these
Carbon atoms are full).
These Carbon atoms are shown in the figure as red circles in the following
link:
https://cp.sync.com/dl/ad3ec80e0#5fnxwjru-7sjjcn5q-5r3p8buu-wb8jn4tx
To this aim, I deleted two Hydrogen atoms and in the next step, I used
antechamber for taxol:
$AMBERHOME/bin/antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc
-s 2
$AMBERHOME/bin/parmchk -i lig.mol2 -f mol2 -o lig.frcmod
The input file (lig.pdb) and the output files (lig.mol2, lig.lib and
lig.frcmod) are as follows:
https://cp.sync.com/dl/1fbba13a0#dq79chn2-7y5wnc8m-cpvadf4k-qzcjyu9e
https://cp.sync.com/dl/50079a740#dckrc4id-zx548z5k-juh4wzz6-da6zeb9n
https://cp.sync.com/dl/92d3ba3b0#fqvwe7ii-mc2gckt8-ykmrvfwp-6vhrtzit
https://cp.sync.com/dl/e55d4bdc0#f5f9ssjr-6mfjiadb-w5zhimcw-xjt7qw5n
To obtain inpcrd and prmtop files, I used following:
---------------------------------------------------------------------------
tleap
source leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 lig.mol2
list
check LIG
loadamberparams lig.frcmod
saveoff LIG lig.lib
set default PBRadii mbondi2
saveamberparm LIG lig.prmtop lig.inpcrd
quit
--------------------------------------------------------------------------
I encountered with
/home/linux/Desktop/amber/amber11/AmberTools/src/leap/tleap
-I: Adding /home/linux/Desktop/amber/amber11/dat/leap/prep to search path.
-I: Adding /home/linux/Desktop/amber/amber11/dat/leap/lib to search path.
-I: Adding /home/linux/Desktop/amber/amber11/dat/leap/parm to search path.
-I: Adding /home/linux/Desktop/amber/amber11/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99SB
----- Source: /home/linux/Desktop/amber/amber11/dat/leap/cmd/leaprc.ff99SB
----- Source of
/home/linux/Desktop/amber/amber11/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters:
/home/linux/Desktop/amber/amber11/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters:
/home/linux/Desktop/amber/amber11/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library:
/home/linux/Desktop/amber/amber11/dat/leap/lib/all_nucleic94.lib
Loading library:
/home/linux/Desktop/amber/amber11/dat/leap/lib/all_amino94.lib
Loading library:
/home/linux/Desktop/amber/amber11/dat/leap/lib/all_aminoct94.lib
Loading library:
/home/linux/Desktop/amber/amber11/dat/leap/lib/all_aminont94.lib
Loading library: /home/linux/Desktop/amber/amber11/dat/leap/lib/ions94.lib
Loading library: /home/linux/Desktop/amber/amber11/dat/leap/lib/solvents.lib
>
> source leaprc.gaff
----- Source: /home/linux/Desktop/amber/amber11/dat/leap/cmd/leaprc.gaff
----- Source of /home/linux/Desktop/amber/amber11/dat/leap/cmd/leaprc.gaff
done
Log file: ./leap.log
Loading parameters: /home/linux/Desktop/amber/amber11/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010)
add. info. at the end
> LIG = loadmol2 lig.mol2
Loading Mol2 file: ./lig.mol2
Reading MOLECULE named LIG
> list
ACE ALA ARG ASH ASN ASP CALA CARG
CASN CASP CCYS CCYX CGLN CGLU CGLY
CHCL3BOX
CHID CHIE CHIP CHIS CILE CIO CLEU CLYS
CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL
CYM CYS CYX Cl- Cs+ DA DA3 DA5
DAN DC DC3 DC4 DC5 DCN DG DG3
DG5 DGN DT DT3 DT5 DTN GLH GLN
GLU GLY HID HIE HIP HIS HOH IB
ILE K+ LEU LIG LYN LYS Li+
MEOHBOX
MET MG2 NALA NARG NASN NASP NCYS NCYX
NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS
NILE NLEU NLYS NMABOX NME NMET NPHE NPRO
NSER NTHR NTRP NTYR NVAL Na+ PHE PL3
POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC
RC3 RC5 RCN RG RG3 RG5 RGN RU
RU3 RU5 RUN Rb+ SER SPC SPCBOX
SPCFWBOX
SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX
TIP4PEWBOX
TP3 TP4 TP5 TPF TRP TYR VAL WAT
frcmod99SBgaff parm99
> check LIG
Checking 'LIG'....
Warning: Close contact of 1.431077 angstroms between .R<LIG 1>.A<C 2> and
.R<LIG 1>.A<C1 3>
Warning: Close contact of 1.430095 angstroms between .R<LIG 1>.A<C 2> and
.R<LIG 1>.A<C12 14>
Warning: Close contact of 1.428651 angstroms between .R<LIG 1>.A<C1 3> and
.R<LIG 1>.A<C2 4>
Warning: Close contact of 1.429862 angstroms between .R<LIG 1>.A<C2 4> and
.R<LIG 1>.A<C13 15>
Warning: Close contact of 1.430451 angstroms between .R<LIG 1>.A<C3 5> and
.R<LIG 1>.A<C4 6>
Warning: Close contact of 1.428858 angstroms between .R<LIG 1>.A<C3 5> and
.R<LIG 1>.A<C14 16>
Warning: Close contact of 1.430266 angstroms between .R<LIG 1>.A<C4 6> and
.R<LIG 1>.A<C5 7>
Warning: Close contact of 1.429907 angstroms between .R<LIG 1>.A<C5 7> and
.R<LIG 1>.A<C15 17>
Warning: Close contact of 1.432359 angstroms between .R<LIG 1>.A<C6 8> and
.R<LIG 1>.A<C7 9>
Warning: Close contact of 1.430581 angstroms between .R<LIG 1>.A<C6 8> and
.R<LIG 1>.A<C9 11>
Warning: Close contact of 1.430581 angstroms between .R<LIG 1>.A<C7 9> and
.R<LIG 1>.A<C8 10>
Warning: Close contact of 1.429222 angstroms between .R<LIG 1>.A<C8 10> and
.R<LIG 1>.A<C10 12>
Warning: Close contact of 1.436972 angstroms between .R<LIG 1>.A<C9 11> and
.R<LIG 1>.A<C11 13>
Warning: Close contact of 1.442121 angstroms between .R<LIG 1>.A<C10 12>
and .R<LIG 1>.A<C11 13>
Warning: Close contact of 1.444989 angstroms between .R<LIG 1>.A<C12 14>
and .R<LIG 1>.A<C25 27>
Warning: Close contact of 1.447672 angstroms between .R<LIG 1>.A<C13 15>
and .R<LIG 1>.A<C25 27>
Warning: Close contact of 1.446810 angstroms between .R<LIG 1>.A<C14 16>
and .R<LIG 1>.A<C24 26>
Warning: Close contact of 1.445294 angstroms between .R<LIG 1>.A<C15 17>
and .R<LIG 1>.A<C24 26>
Warning: Close contact of 1.220762 angstroms between .R<LIG 1>.A<C42 44>
and .R<LIG 1>.A<O5 54>
Warning: Close contact of 1.220790 angstroms between .R<LIG 1>.A<C43 45>
and .R<LIG 1>.A<O6 55>
Warning: Close contact of 1.230974 angstroms between .R<LIG 1>.A<C45 47>
and .R<LIG 1>.A<O3 52>
Warning: Close contact of 1.227794 angstroms between .R<LIG 1>.A<C46 48>
and .R<LIG 1>.A<O4 53>
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: n - c2 - c1
Could not find angle parameter: n - c2 - o
Could not find angle parameter: c1 - c2 - o
Could not find angle parameter: c3 - c1 - os
Could not find angle parameter: c3 - c1 - os
Could not find angle parameter: cy - os - c1
Could not find angle parameter: c3 - c1 - os
There are missing parameters.
check: Warnings: 22
Unit is OK.
> loadamberparams lig.frcmod
Loading parameters: ./lig.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff LIG lig.lib
Creating lig.lib
Building topology.
Building atom parameters.
> set default PBRadii mbondi2
Using H(N)-modified Bondi radii
> saveamberparm LIG lig.prmtop lig.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 33 62 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 39 40 duplicates bond ('triangular' bond) or angle ('square'
bond)
Building improper torsion parameters.
total 5 improper torsions applied
Building H-Bond parameters.
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
LIG 1
)
(no restraints)
> quit
-------------------------------------------------------------------------------------------
I ignored the warnings after check LIG. Is it correct?
Based on tutorial on
http://ambermd.org/tutorials/advanced/tutorial3/index.htm (MM-PBSA), I
created prmtop and inpcrd file pairs for protein, ligand, complex and
solvated complex (totally, 8 files).
According to the tutorial, I used prmtop and inpcrd files for solvated
complex.
For minimization step, I used ambertools 14, using following commands:
mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i min.in -o min.out -p
comp_sol.prmtop -c comp_sol.inpcrd -r min.rst -ref comp_sol.inpcrd -inf
min_info
The min.in file is as follows:
minimized complex_solvated
&cntrl
imin=1,maxcyc=4000,ncyc=2000,
cut=10.0,ntb=1,
ntc=1,ntf=2,
ntpr=100,
ntr=1,restraintmask=':1-124',
restraint_wt=2.0
/
After 2 minutes, I encountered with:
[compute-0-2:20023] *** Process received signal ***
[compute-0-2:20023] Signal: Segmentation fault (11)
[compute-0-2:20023] Signal code: Address not mapped (1)
[compute-0-2:20023] Failing at address: 0x7fc16d7c52b8
[compute-0-2:20023] [ 0] /lib64/libpthread.so.0() [0x3c1d80f710]
[compute-0-2:20023] [ 1]
/share/apps/2_amber/amber14/bin/sander.MPI(nb_adjust_+0x6d3) [0x575763]
[compute-0-2:20023] [ 2]
/share/apps/2_amber/amber14/bin/sander.MPI(ewald_force_+0x1373) [0x578683]
[compute-0-2:20023] [ 3]
/share/apps/2_amber/amber14/bin/sander.MPI(force_+0x470d) [0x7cd78d]
[compute-0-2:20023] [ 4]
/share/apps/2_amber/amber14/bin/sander.MPI(sander_+0x7a86) [0x4f915e]
[compute-0-2:20023] [ 5]
/share/apps/2_amber/amber14/bin/sander.MPI(MAIN__+0xd3b) [0x4f1643]
[compute-0-2:20023] [ 6]
/share/apps/2_amber/amber14/bin/sander.MPI(main+0x2a) [0xbc734a]
[compute-0-2:20023] [ 7] /lib64/libc.so.6(__libc_start_main+0xfd)
[0x3c1d01ed5d]
[compute-0-2:20023] [ 8] /share/apps/2_amber/amber14/bin/sander.MPI()
[0x465659]
[compute-0-2:20023] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 20023 on node compute-0-2.local
exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
The last lines of out file is follows:
BOND = 7994.9968 ANGLE = 1942.7203 DIHED =
1307.6143
VDWAALS = 10115.3339 EEL = ************* HBOND =
0.0000
1-4 VDW = 1048.5709 1-4 EEL = 6660.6152 RESTRAINT =
226.7095
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
1800 -6.8566E+07 2.0256E+11 2.9159E+13 H2 5140
BOND = 7994.9968 ANGLE = 1942.7203 DIHED =
1307.6143
VDWAALS = 10115.3337 EEL = ************* HBOND =
0.0000
1-4 VDW = 1048.5709 1-4 EEL = 6660.6152 RESTRAINT =
226.7095
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
1900 -2.2747E+08 2.2450E+12 3.2318E+14 H2 5140
BOND = 7994.9968 ANGLE = 1942.7203 DIHED =
1307.6143
VDWAALS = 10115.3338 EEL = ************* HBOND =
0.0000
1-4 VDW = 1048.5709 1-4 EEL = 6660.6152 RESTRAINT =
226.7095
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -9.7339E+07 4.0944E+11 5.8939E+13 O 5339
BOND = 7994.9968 ANGLE = 1942.7203 DIHED =
1307.6143
VDWAALS = 10115.3340 EEL = ************* HBOND =
0.0000
1-4 VDW = 1048.5709 1-4 EEL = 6660.6152 RESTRAINT =
226.7095
EAMBER = *************
Please guide me to resolve this problem.
Best regards,
Shahab
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Received on Sun Sep 25 2016 - 02:30:02 PDT
