Dear Andy,
Thank you for your answer! Your suggestions made it possible to spot the problem (I think).
When trying QM/MM with an internal QM method, it appears that the atom type of three oxygens from my ligand are unknown. Here is the error message:
QMMM: Atom number: 107 has atomic number -1
My ligand is GTP and the three oxygen atoms bonded to the gamma phosphorus have no atom type.. It is odd as leap didn’t complain about it when I generated the topology file (well, now I see in the leap.log file that it didn’t find a type for these oxygen atoms..). Nevertheless, the topology file of the previous structure was generated with Amber11 (if I remember well) and there wasn’t this problem. It looks like my .frcmod file wasn’t taken into account by leap..
Any idea how to fix this?
Here are informative parts of the leap.log file:
> source oldff/leaprc.ff99bsc0
> loadoff mga.lib
Loading library: ./mga.lib
Loading: MGA
> loadamberprep gtp.prep
Loading Prep file: ./gtp.prep
(UNKNOWN ATOM TYPE: O3)
(UNKNOWN ATOM TYPE: O3)
(UNKNOWN ATOM TYPE: O3)
Loaded UNIT: GTP
> loadamberparams gtp.frcmod
Loading parameters: ./gtp.frcmod
Reading force field modification type file (frcmod)
Reading title:
# Modifications to the AMBER94 force field for polyphosphates
(UNKNOWN ATOM TYPE: O3)
> mol=loadpdb native_minNR.pdb
Loading PDB file: ./native_minNR.pdb
total atoms in file: 2942
> solvateoct mol TIP3PBOX 14.0
Scaling up box by a factor of 1.239416 to meet diagonal cut criterion
Solute vdw bounding box: 42.615 39.499 52.879
Total bounding box for atom centers: 87.583 87.583 87.583
(box expansion for 'iso' is 33.7%)
> addions mol Na+ 0
10 Na+ ions required to neutralize.
Adding 10 counter ions to "mol" using 1A grid
Total solute charge: -10.00 Max atom radius: 2.10
Grid extends from solute vdw + 4.15 to 10.25
Box:
enclosing: -31.47 -34.18 -30.88 31.56 36.94 26.04
sized: 96.53 93.82 97.12
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 0 sec
Volume = 2.32% of box, grid points 48685
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 4 sec
(Replacing solvent molecule)
Placed Na+ in mol at (-0.64, 8.57, -20.43).
(Replacing solvent molecule)
Placed Na+ in mol at (-4.67, -13.05, 13.57).
(Replacing solvent molecule)
Placed Na+ in mol at (-6.67, 25.12, -5.01).
(Replacing solvent molecule)
Placed Na+ in mol at (11.74, 12.49, -13.96).
(Replacing solvent molecule)
Placed Na+ in mol at (-8.50, 4.60, -19.65).
(Replacing solvent molecule)
Placed Na+ in mol at (-17.68, -14.72, 2.82).
(Replacing solvent molecule)
Placed Na+ in mol at (9.47, -17.00, -10.59).
(Replacing solvent molecule)
Placed Na+ in mol at (-19.10, 4.66, -13.29).
(Replacing solvent molecule)
Placed Na+ in mol at (0.64, 23.66, -8.98).
(Replacing solvent molecule)
Placed Na+ in mol at (-9.34, -21.60, 9.38).
Done adding ions.
> saveamberparm mol nat2-0_minNR.parm nat2-0_minNR.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for NC-CB-CB-N*
atoms are: N3 C5 C4 N9
** Warning: No sp2 improper torsion term for NB-C-CB-CB
atoms are: N7 C6 C5 C4
old PREP-specified impropers:
<GTP 169>: C8 C4 N9 C1'
<GTP 169>: C5 N1 C6 O6
<GTP 169>: C6 C2 N1 H1
<GTP 169>: C2 H21 N2 H22
<GTP 169>: N7 N9 C8 H8
<GTP 169>: N1 N3 C2 N2
total 575 improper torsions applied
6 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
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
CARG 1
CSER 1
NMET 2
WAT 9255
)
(no restraints)
I’m using Amber and Ambertools 16 in a cluster where I cannot personally update the software..
Thank you for any help,
Sincerely,
Ruth
> On 08 Feb 2018, at 22:52, Goetz, Andreas <agoetz.sdsc.edu> wrote:
>
> Hi Ruth,
>
> The error message in sander just states that Orca did not produce a valid output file, i.e. something went wrong during the execution of Orca. From what you describe, it does sound like sander wrote an invalid input file for Orca. You said that you have tested the setup for you system before and it worked - can you confirm that your sander input file is indeed identical to your previous tests that worked? Does QM/MM with an internal QM method work? What happens if you switch off smd?
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
>> On Feb 8, 2018, at 3:37 PM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>>
>> Dear Amber users,
>>
>> I’m trying to run a SMD simulation of a protein-ligand complex in explicit solvent using the following input file:
>>
>> SMD LCOD rxn coord using Orca
>> &cntrl
>> imin=0,
>> irest=1, ntx=5,
>> ntb=2, pres0=1.0, ntp=1, taup=1.0,
>> cut=12.0,
>> tempi=300.0, temp0=300.0,
>> ntt=3, gamma_ln=2.0, ig=-1,
>> nstlim=100000, dt=0.0005,
>> ntpr=100, ntwx=100, ntwr=1000, ioutfm=1,
>> ntc=2, ntf=2,
>> noshakemask = '.2646-2689,2828-2851,2941-2946,11881-11883,14608-14610',
>> ntr=1,
>> restraintmask = ':170,185,@CA,C,N',
>> restraint_wt=5.0,
>> ifqnt=1, infe=1
>> /
>> &qmmm
>> qmmask = ':168,169,179,196-197,3176,4085',
>> qmcharge=0,
>> qm_theory='EXTERN',
>> qmshake=0,
>> qmcut=17.0,
>> /
>> &orc
>> method='PBE',
>> basis=‘def2-SVP’,
>> cbasis=‘def2-SVP’,
>> jbasis=‘def2-SVP',
>> num_threads=1,
>> convkey=’TIGHTSCF’,
>> dipole=1,
>> maxiter=150,
>> /
>> &smd
>> output_file = 'nat_smdo25-1_198.txt'
>> output_freq = 20
>> cv_file='cv_nat-1_198.in'
>> /
>>
>> Previously, I was encountering energy convergence problems within Orca and in my last attempt to solve this issue, I took a further minimised structure, solvated it in a 14 A octahedron box, minimised the solvent, heated the system from 0 to 300K. Now that I want to proceed with the SMD, the calculation is not even starting, I got this very odd message that I didn’t get before in the orc_job.dat file:
>>
>> Error: XYZ File is for simple coordinate input only
>> Unknown atom specifier: -2.8123014350914630 0.9725245871287427 0.8684715494137160
>> [file orca_tools/Tool-Scanner/qcscancoord.cpp, line 30]:
>>
>> Apparently somehow Amber is not building “readable” inputs for Orca (?) Which is odd because this was not the case before.. Here is the error message in the amber output file (if useful):
>>
>> SANDER BOMB in subroutine read_results (qm2_extern_orc_module)
>> Error reading Orca output from file orc_job.engrad
>> (Current total energy or gradient not found or unsupported units.)
>>
>> Thank you in advance for any help in solving this issue,
>>
>> Sincerely,
>>
>> Ruth
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 09 2018 - 02:30:02 PST
