Please find in attachment the files you need.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Friday, May 16, 2014 3:43 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Analysis of minimization stage
as attachments, please. We can't do much with the files pasted into an email.
On May 16, 2014, at 8:58 AM, Valentina Romano <valentina.romano.unibas.ch> wrote:
> 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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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 16 2014 - 07:00:04 PDT
