Dear David, the calculation crashes while reading atomic coordinates and
velocities with the error message that I reported before.
Executable path: pmemd.cuda
| Working directory: /home/alicia/COX
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: heat.in
| MDOUT: cox2_aanpoxb_heat.out
| INPCRD: cox2_aanpoxb_min2.rst
| PARM: cox2_aanpoxb.prmtop
| RESTRT: cox2_aanpoxb_heat.rst
| REFC: cox2_aanpoxb_min2.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: cox2_aanpoxb_heat.nc
| MDINFO: mdinfo
| MDFRC: mdfrc
"cox2_aanpoxb_heat.out" 247 lÃneas --0%-- 1,0-1
Comienzo
tol = 0.00001
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 120.473 Box Y = 120.473 Box Z = 120.473
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 128 NFFT2 = 128 NFFT3 = 128
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
default_name
Mask .CA,C,O,N; matches 38857 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 11500000 0.000000 300.000000 0 0
RESTRAINTS:
Requested file redirections:
DISANG = rest
Restraints will be read from file: rest
Here are comments from the DISANG input file:
Number of restraints read = 2
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 34445
2017-02-22 19:57 GMT-03:00 Alicia Merlino <amerlino.fcien.edu.uy>:
> Hi David, thank you for your advice. I ran parmed and the prmtop is ok.
> I´m using the same prmtop for minimization and heating but during
> minimization SHAKE was turned off. I´ll try to make the heating with ntpr=1
> to get more information. I´m using Amber14 implemented on the Amber package
> with the ff14SB force field for the protein.
>
> 2017-02-22 17:49 GMT-03:00 David Case <david.case.rutgers.edu>:
>
>> On Wed, Feb 22, 2017, Alicia Merlino wrote:
>> >
>> > 80: 177 - 178 and 81: 177 - 179
>> > Hydrogen atom 177 appears to have multiple bonds to atoms 178 and 179
>> which
>> > is illegal for SHAKEH.
>> > Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
>>
>> As Hai suggested, use parmed to look at atoms 177 to 179 (which appear to
>> be CA, HA2 and HA3 in a glycine). I admit that this looks like a very
>> odd error. Is there any chance that the prmtop file has changed between
>> the
>> minimization and heating steps? Does the error happen on the very first
>> step
>> of heating (try to make a very short and simple test case, with ntpr=1,
>> to get the most information.) Did you have SHAKE turned on during the
>> minimization?
>>
>> Also, can you say what program you are running, and what version of Amber?
>> I'm having trouble finding the location in the code of the errors you
>> report above.
>>
>> ...thx...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Dra. Alicia Merlino
> Profesora Adjunta del Laboratorio de Qca. Teórica y Computacional
> Instituto de Química Biológica
> Facultad de Ciencias, Universidad de la República
> Iguá 4225, 11400 Montevideo, Uruguay
> Tel: (+598) 2525 2186 <+598%202525%202186>
> Fax: (+598) 2525 0749 <+598%202525%200749>
>
--
Dra. Alicia Merlino
Profesora Adjunta del Laboratorio de Qca. Teórica y Computacional
Instituto de Química Biológica
Facultad de Ciencias, Universidad de la República
Iguá 4225, 11400 Montevideo, Uruguay
Tel: (+598) 2525 2186
Fax: (+598) 2525 0749
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Received on Wed Feb 22 2017 - 15:30:02 PST
