Goodmorning,
I have just run the 'checkoverlap' command and, as expected there are
numerous (dozen of hundreds) warnings with value dramatically short.
.........................................................................................................................
2 Warning: Atoms 5115:ARG_312.N and 36285:WAT_8745.H2 are close (0.52)
2 Warning: Atoms 5124:ARG_312.HG3 and 63241:WAT_17731.O are close (0.40)
2 Warning: Atoms 5124:ARG_312.HG3 and 63243:WAT_17731.H2 are close
(0.69)
2 Warning: Atoms 5176:MET_315.HB2 and 36734:WAT_8895.H1 are close (0.75)
2 Warning: Atoms 5224:ALA_318.O and 62866:WAT_17606.O are close (0.66)
2 Warning: Atoms 5224:ALA_318.O and 62867:WAT_17606.H1 are close (0.34)
2 Warning: Atoms 5228:LYS_319.HA and 62973:WAT_17641.H2 are close (0.58)
2 Warning: Atoms 5277:TYR_322.N and 51270:WAT_13740.H2 are close (0.43)
................................................................................................................................
I really don't knwo what's going on, the only try remaining is to change
the machine running the calculation.
Have you guys got an idea of what is going on?
This is the *mdinfo*:
NSTEP = 500000 TIME(PS) = 1000.000 TEMP(K) = 298.00 PRESS =
0.0
Etot = 48357.7411 EKtot = 64961.1600 EPtot =
-16603.4189
BOND = 1953.0563 ANGLE = 4708.7175 DIHED =
9197.0051
1-4 NB = 2989.7399 1-4 EEL = 31153.1436 VDWAALS =
-2016.9171
EELEC = -69163.1697 EHBOND = 0.0000 RESTRAINT =
4575.0057
EAMBER (non-restraint) = -21178.4246
Ewald error estimate: 0.1085E+01
These are few steps from the *output*:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -32032.5985 EKtot = 0.0000 EPtot =
-32032.5985
BOND = 230.1502 ANGLE = 2214.4942 DIHED =
8832.3438
1-4 NB = 3022.5901 1-4 EEL = 31924.2094 *VDWAALS* =
-2016.9171
EELEC = -76239.4690 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1436E+01
------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 147.67 PRESS =
0.0
Etot = 14429.2449 EKtot = 32191.1524 EPtot =
-17761.9074
BOND = 2293.4897 ANGLE = 4978.1187 DIHED =
9561.7504
1-4 NB = 3116.9234 1-4 EEL = 31209.3800 *VDWAALS* =
-2016.9171
EELEC = -72596.0372 EHBOND = 0.0000 RESTRAINT =
5691.3847
EAMBER (non-restraint) = -23453.2922
Ewald error estimate: 0.1254E+01
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 227.30 PRESS =
0.0
Etot = 37405.5600 EKtot = 49548.6882 EPtot =
-12143.1281
BOND = 3072.0214 ANGLE = 6129.2122 DIHED =
9740.1173
1-4 NB = 3146.5469 1-4 EEL = 31001.3755 *VDWAALS* =
-2016.9171
EELEC = -71063.0644 EHBOND = 0.0000 RESTRAINT =
7847.5801
EAMBER (non-restraint) = -19990.7082
Ewald error estimate: 0.1187E+01
------------------------------------------------------------------------------
*VDWAALS *has no fluctuations at all....this made me curious....
V
On Wed, Oct 10, 2018 at 10:48 PM Vito GENNA <vito.genna.irbbarcelona.org>
wrote:
> Dear David,
>
> Thank you for your prompt reply.
> Well, I have visually inspected the system by opening, with VMD, the
> topology and the md.nc file.
> I will make a try with the command you suggested.
> The strange parameter in the output is the super-stable (the same value)
> of the vdw.
>
> I’ll get back to you ASAP.
>
> Thanks in advance.
>
> Vito
>
>
>
>
> *Vito Genna, Ph.D*
> *EMBO Fellow*
> Scientist
> Molecular Modelling and Bioinformatics
> Orozco Lab
>
> *Dep. of Structural and Computational Biology*
> *Institute for Research in Biomedicine (IRB Barcelona)*
> Parc Científic de Barcelona
> C/ Baldiri Reixac 10-12
> 08028 Barcelona
>
> P.S. Email written with my IPhone. Sorry for typo.
>
> Il giorno 10 ott 2018, alle ore 22:16, David A Case <
> david.case.rutgers.edu> ha scritto:
>
> On Wed, Oct 10, 2018, Vito GENNA wrote:
>
> Once i got the system I minimize it and what I note is that water molecules
>
> dramatically overlap protein's atoms.
>
>
> What is the evidence that this is happening? Did you visualize the
> system? Calculate the distance from a given water molecule to a given
> protein atom? Something else?
>
> You can use the "checkoverlap" command in cpptraj to print out all short
> contacts. There should be very few of these following minimization. It
> would probably also be more helpful to see the *output* from
> minimization, rather than the input file.
>
> Look carefully at the minimization and heating outputs for evidence of
> problems. It looks like you have 750 residues in your protein: is that
> correct? You might try a short calculation on a smaller fragment. I
> didn't notice anything wrong with your tleap input, but I could be
> missing something.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
***********************************************************************
*Vito Genna, Ph.D*
*EMBO Fellow*
*Postoctoral Researcher*
*Molecular Modeling and Bioinformatics*
*Orozco Lab*
*Institute for Research in Biomedicine (IRB Barcelona)*
*Parc Centific de Barcelona*
*C/ Baldiri Reixac 10-12*
*08028 Barcelona*
***********************************************************************
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Received on Thu Oct 11 2018 - 02:00:02 PDT
