Hi
>I think you will have to post your prmtop and coordinate files (after
>minimization). But first, look to see what atoms 6 and 14 are -- are they
>supposed to be bonded to each other? And, just for sanity sake, re-run
>the MD with tempi=0.0 and ntt=0. But it looks like there is something
>very wrong with the way your ligand is constructed, but something that
>cannot be debugged without seeing the actual files.
The atoms 6 and 14 are N6 and H62 and they are bonded to each other (they are the N and the second H of the NH2 group).
The prmtop file for the ligand (6-amino purine) is:
%VERSION VERSION_STAMP = V0001.000 DATE = 05/02/14 13:50:04
%FLAG TITLE
%FORMAT(20a4)
D6A
%FLAG POINTERS
%FORMAT(10I8)
15 4 5 11 9 15 16 23 0 0
67 1 11 15 23 11 19 7 8 0
0 0 0 0 0 0 0 0 15 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
N9 C8 N7 C5 C6 N6 N1 C2 N3 C4 HN9 H8 H61 H62 H2
%FLAG CHARGE
%FORMAT(5E16.8)
-6.90625170E+00 7.26523101E+00 -9.86008653E+00 -4.32232956E+00 1.39801486E+01
-1.75389638E+01 -1.45413954E+01 1.25533425E+01 -1.34298351E+01 8.32394664E+00
5.80744701E+00 1.32658344E+00 8.20550169E+00 8.20550169E+00 9.49381830E-01
%FLAG ATOMIC_NUMBER
%FORMAT(10I8)
7 6 7 6 6 7 7 6 7 6
1 1 1 1 1
%FLAG MASS
%FORMAT(5E16.8)
1.40100000E+01 1.20100000E+01 1.40100000E+01 1.20100000E+01 1.20100000E+01
1.40100000E+01 1.40100000E+01 1.20100000E+01 1.40100000E+01 1.20100000E+01
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 2 2 1 1 2 1 2
3 4 3 3 4
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
9 7 8 10 8 5 6 3 3 3
1 1 1 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 2 3 5 8 4 5
6 9 7 8 9 10
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
D6A
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
4.38800000E+02 4.70300000E+02 4.06600000E+02 4.94600000E+02 3.56000000E+02
4.92900000E+02 4.78400000E+02 4.49000000E+02 4.83100000E+02 4.01200000E+02
3.47200000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.37100000E+00 1.35000000E+00 1.01100000E+00 1.33500000E+00 1.07900000E+00
1.33600000E+00 1.38700000E+00 1.36400000E+00 1.34200000E+00 1.01400000E+00
1.08500000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
7.47800000E+01 4.97600000E+01 7.02100000E+01 7.06000000E+01 6.84600000E+01
4.69900000E+01 7.22400000E+01 5.01300000E+01 7.01400000E+01 6.93400000E+01
6.91600000E+01 6.71800000E+01 4.90800000E+01 6.85900000E+01 7.32000000E+01
7.07800000E+01 5.17600000E+01 4.76300000E+01 4.00500000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.95511867E+00 2.13104793E+00 2.06542352E+00 2.21779083E+00 1.97484090E+00
2.19318168E+00 1.84079955E+00 2.18829475E+00 2.08950908E+00 2.09666493E+00
2.14029818E+00 2.09387240E+00 2.02685173E+00 2.02213934E+00 2.04116344E+00
2.21988523E+00 2.03069145E+00 2.19195995E+00 2.00451150E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
4.75000000E+00 3.62500000E+00 4.80000000E+00 3.00000000E-01 1.70000000E+00
1.05000000E+00 5.00000000E+03
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00 3.14159400E+00
%FLAG SCEE_SCALE_FACTOR
%FORMAT(5E16.8)
1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
1.20000000E+00 0.00000000E+00
%FLAG SCNB_SCALE_FACTOR
%FORMAT(5E16.8)
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00 0.00000000E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
9.44293233E+05 8.82619071E+05 8.19971662E+05 2.12601181E+03 2.27577561E+03
1.39982777E-01 5.46147253E+04 5.30987710E+04 4.90239937E+01 2.43828624E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
8.01323529E+02 6.53361429E+02 5.31102864E+02 2.09604198E+01 1.82891803E+01
9.37598976E-02 1.05031585E+02 8.73413012E+01 1.73473071E+00 1.20953369E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 30 3 3 33 5 15 36 10 15
39 10 21 42 11
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 1 0 27 2 3 6 4 6
9 6 9 12 7 9 27 7 12 15
8 12 18 9 18 21 9 21 24 9
24 27 9
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
0 3 33 2 3 0 30 6 6 3
33 8 12 15 36 13 12 15 39 13
18 21 42 17 24 21 42 17 27 0
30 18 36 15 39 19
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 6 1 0 27 9 3 0 27
24 4 3 0 27 5 3 6 9 7
6 9 12 9 6 9 27 9 9 12
15 10 9 12 18 11 9 27 24 11
12 9 27 12 12 18 21 14 15 12
18 15 18 21 24 16 21 24 27 14
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
30 0 3 6 5 9 6 3 33 1
9 12 15 36 6 9 12 15 39 6
30 0 27 9 4 12 18 21 42 3
18 12 15 36 6 18 12 15 39 6
30 0 27 24 4 27 0 3 33 5
27 24 21 42 3 30 0 3 33 5
30 0 -3 -27 7 33 0 -3 -6 7
12 36 -15 -39 7 42 18 -21 -24 7
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 3 -6 9 1 0 27 -9 6 2
0 27 9 12 2 0 27 24 21 3
3 0 -27 9 4 3 0 27 24 4
3 6 9 12 3 3 6 -9 27 3
27 0 -3 6 5 6 9 12 15 2
6 9 12 18 2 6 9 27 24 2
9 12 18 21 3 9 27 -24 21 3
12 9 27 24 2 12 18 -21 24 3
15 12 9 27 2 15 12 18 21 3
18 12 9 27 2 18 21 -24 27 3
12 27 -9 -6 7 9 18 -12 -15 7
9 0 -27 -24 7
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 8 9 10 11 12 3
4 5 9 10 11 12 4 5 6 7
9 10 11 12 5 6 7 8 9 10
11 12 13 14 6 7 8 9 10 13
14 15 7 8 10 13 14 8 9 10
13 14 15 9 10 15 10 11 15 11
12 15 12 0 14 0 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
na cc nd ca ca nh nb ca nb ca hn h5 hn hn h5
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.55000000E+00 1.70000000E+00 1.55000000E+00 1.70000000E+00 1.70000000E+00
1.55000000E+00 1.55000000E+00 1.70000000E+00 1.55000000E+00 1.70000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.90000000E-01 7.20000000E-01 7.90000000E-01 7.20000000E-01 7.20000000E-01
7.90000000E-01 7.90000000E-01 7.20000000E-01 7.90000000E-01 7.20000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
%FLAG IPOL
%FORMAT(1I8)
0
The minimization of the ligand itself was ran as follows:
&cntrl
imin=1,
maxcyc=500,
ntmin=3,
ntb=0,
igb=0,
cut=999.0,
ntpr=1, ntwx=1, ntwr=100
The rst file after min is:
D6A
15
93.8783892 -5.0181024 21.1435893 92.6343838 -5.1977371 21.7185542
91.8061611 -5.9034681 20.9135884 92.5912700 -6.1382488 19.8456173
92.3168646 -6.8180191 18.6754697 91.1382816 -7.3776395 18.4304966
93.1870764 -6.9806930 17.6897614 94.3890138 -6.4200022 17.9190746
94.7721874 -5.7353384 19.0167879 93.8357989 -5.6174753 19.9617453
94.6723371 -4.5363390 21.5202039 92.3815452 -4.8102723 22.6945684
91.0306396 -7.8508727 17.5533760 90.4300143 -7.2910720 19.1395420
95.1320371 -6.5307201 17.1346250
I also ran a MD as you suggested (tempi=0.0 and ntt=0):
1ps MD Adenine
&cntrl
imin=0,
irest=0,
ntx=1,
ig=-1,
ntb=0,
cut=999.0,
ntc=2,
ntf=2,
tempi=0.0,
temp0=300.0,
ntt=0,
nstlim=1000, dt=0.001,
ntpr=1, ntwx=1, ntwr=1000
Sander stopped at step number 5:
vlimit exceeded for step 5; vmax = 162.4988
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 4 6 14
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I built the prmtop and the initial coord files using antechamber and i am wondering the error was done at that step.
Thank you a lot for helping me.
Vale
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Received on Fri May 16 2014 - 06:30:02 PDT
