Dear David,
Thanks for your reply.
At first I removed the CONECT cards from the lig.pdb file. Then I used
"acdoctor -i lig.pdb -f pdb"
The result of acdoctor is as follows:
-----------------------------------------------------------
-- Check Format for pdb,mpdb or ac File --
-- Status: pass --
-- Check Unusual Elements --
-- Status: pass --
-- Check Open Valences --
-- Check Geometry --
-- For those bonded --
-- For those unbonded --
-- Status: pass --
-- check weird bonds --
-- Status: pass --
-- Check if the input is only one unit --
-- Status: pass --
-- Now try to judge bond type --
Running: /share/apps/amber/amber14/bin/bondtype -j full -
i ACDOCTOR_INIT.ac -o
ACDOCTOR_BOND.ac -f ac
-- Now try to assign atom type --
Running: /share/apps/amber/amber14/bin/atomtype -i ACDOCT
OR_BOND.ac -o
ACDOCTOR_ATOM.ac -p gaff
-- Now write out ACDOCTOR.mol2 --
-- IF no error occurs in bond and atom type assignments,
lig.pdb should have no problem for the antechamber pack
age. --
ACDOCTOR_INIT.ac : ac file before bond type and atom type
assignment
ACDOCTOR_BT.ac : ac file after bond type assignment
ACDOCTOR_AT.ac : ac file after gaff atom type assignment
ACDOCTOR_SYBYL.ac : ac file after sybyl atom type assignmen
t
ACDOCTOR.mol2 : mol2 file after sybyl atom type assignm
ent
-------------------------------------------------------------
It seemed all things were ok. Then I used
$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
---------------------------------------------------------------------------
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
-------------------------------------------------------------
-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'....
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
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
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 27 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)
----------------------------------------------------------------------------
This time (without connect card in pdb file), check LIG is ok and there are
no warning after check LIG.
----------------------------------------------------------------------------
The lig.pdb, lig.mol2 and lig.frcmod files is as follows:
https://ln.sync.com/dl/a88eb2290#fwqn5kc5-8tupq9vn-4skufbzb-iyjfi4fx
https://ln.sync.com/dl/9acac5650#ydqiugah-n7ie8zdh-fmagxig8-a6g5djmw
https://ln.sync.com/dl/ea2164ae0#sihx9cdd-ks6u7bat-znxw7car-pj7pmv2q
-----------------------------------------------------------------------------
After using "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",
*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x7f63add2b628
[ 0] /lib64/libpthread.so.0() [0x3e29c0f710]
[ 1] /share/apps/2_amber/amber14/bin/sander.MPI(nb_adjust_+0x6d3) [0x575763]
[ 2] /share/apps/2_amber/amber14/bin/sander.MPI(ewald_force_+0x1373)
[0x578683]
[ 3] /share/apps/2_amber/amber14/bin/sander.MPI(force_+0x470d) [0x7cd78d]
[ 4] /share/apps/2_amber/amber14/bin/sander.MPI(sander_+0x7a86) [0x4f915e]
[ 5] /share/apps/2_amber/amber14/bin/sander.MPI(MAIN__+0xd3b) [0x4f1643]
[ 6] /share/apps/2_amber/amber14/bin/sander.MPI(main+0x2a) [0xbc734a]
[ 7] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e2941ed5d]
[ 8] /share/apps/2_amber/amber14/bin/sander.MPI() [0x465659]
*** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 19668 on node compute-0-0.local
exited on signal 11 (Segmentation fault).
-------------------------------------------------------------------------------------------------
Is Segmentation fault related to following lines in " saveamberparm LIG
lig.prmtop lig.inpcrd "?
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)
I'm really confused. How to resolve this issue?
Best,
Shahab
On Tue, Sep 27, 2016 at 4:34 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Sep 26, 2016, shahab shariati wrote:
> >
> > I'm really confused. I used antechamber for 5 other ligands without any
> > problems.
>
> Remove the CONECT cards from the lig.pdb file. These cards have many, many
> repeated entries; looking at just the top few here:
>
> CONECT 1 38 46 64
> CONECT 2 3
> CONECT 2 3
> CONECT 2 3
> CONECT 2 3
> CONECT 2 14
> CONECT 2 14
> CONECT 2 14
> CONECT 2 14
> CONECT 2 65
> CONECT 3 2
> CONECT 3 2
> CONECT 3 2
> CONECT 3 2
> CONECT 3 4
> CONECT 3 4
> CONECT 3 4
> CONECT 3 4
> CONECT 3 66
> CONECT 4 3
> CONECT 4 3
> CONECT 4 3
> CONECT 4 3
>
> I'm not sure if it is the duplicated entries, or errors in the
> connectivity that is the problem, but they are confusing antechamber,
> which should work OK after the change.
>
> Note: running the "acdoctor" program on troublesome input is highly
> recommended:
>
> acdoctor -i lig.pdb -f pdb
>
> In the next release, antechamber will automatically run acdoctor to try to
> identify problems, and give more helpful error messages.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 28 2016 - 06:00:05 PDT
