[gmx-users] g-dist

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Tue Dec 21 14:52:15 CET 2010 

Dear Justin

WARNING 1 [file g-dist.mdp, line unknown]:
  Can only use nstype=Simple with pbc=no, setting nstype to Simple
WARNING 2 [file complex.top, line 39718]:
  Bad box in file complex.gro

Generated a cubic box   10.816 x   14.959 x    9.086
Warning: atom name 6439 in complex.top and complex.gro does not match (C18 -
H9N)
Warning: atom name 6440 in complex.top and complex.gro does not match (C6 -
H9O)
Warning: atom name 6441 in complex.top and complex.gro does not match (C11 -
H19)
Warning: atom name 6442 in complex.top and complex.gro does not match (H11 -
C18)
Warning: atom name 6443 in complex.top and complex.gro does not match (C15 -
C6)
Warning: atom name 6444 in complex.top and complex.gro does not match (H15 -
C11)
Warning: atom name 6445 in complex.top and complex.gro does not match (C17 -
H11)
Warning: atom name 6446 in complex.top and complex.gro does not match (F1 -
C15)
Warning: atom name 6447 in complex.top and complex.gro does not match (C16 -
H15)
Warning: atom name 6448 in complex.top and complex.gro does not match (H16 -
C17)
Warning: atom name 6449 in complex.top and complex.gro does not match (C12 -
F1)
Warning: atom name 6450 in complex.top and complex.gro does not match (H12 -
C16)

WARNING 3 [file complex.top, line 39718]:
  12 non-matching atom names
  atom names from complex.top will be used
  atom names from complex.gro will be ignored

besides I generated it as enzyme/drug tutorial.
besides C12 is in line 2 from the end of the page.
thanks in advance





On Tue, Dec 21, 2010 at 5:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear justin
>> after using grompp without -maxwarn I faced these:
>>
>> NOTE 2 [file g-dist.mdp, line unknown]:
>>  You are using a plain Coulomb cut-off, which might produce artifacts.
>>  You might want to consider using PME electrostatics.
>>
>>
>> This run will generate roughly 2 Mb of data
>> writing run input file...
>>
>> There were 2 notes
>>
>> There were 3 warnings
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.0.7
>> Source code file: ../../../../src/gmxlib/gmx_fatal.c, line: 481
>>
>> Fatal error:
>> Too many warnings (3), grompp terminated.
>> If you are sure all warnings are harmless, use the -maxwarn option.
>>
>>
> None of this output actually indicates what the errors are.  I don't know
> if any of it will be relevant to the problem at hand, but without seeing
> what the errors are, there's no way to rule out incorrect input.
>
>
>  besides it is in 6454 line of complex.gro
>>
>>
> How did you generate complex.gro?  If it is line 6454, it is not numbered
> accordingly.  That doesn't matter, in theory, but if you've just simply
> concatenated the protein and ligand coordinate files and left any extraneous
> information in the .gro file, it could be causing the error.
>
> -Justin
>
>
>>
>>
>>
>>
>> On Tue, Dec 21, 2010 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    mohsen ramezanpour wrote:
>>
>>        Dear All
>>        I did the Enzyme/drug tutorial and generated complex.gro and
>>        complex.top files as was said.
>>        Now I want to measure the distance between center of mass of
>>        protein and drug
>>        I used g_dist but I could not.
>>        I entered these commands(of course I made an index.ndx and
>>        g-dist.tpr):
>>
>>        I used from an typical .mdp file to generate .tpr file by below
>>        command:
>>
>>        grompp  -c complex.gro     -p   complex.top   -o  g-dist.tpr
>>           -f    g-dist.mdp    -maxwarn 3
>>
>>
>>    What warnings are you ignoring?  This is, in general, a very bad idea.
>>
>>
>>        then,
>>        g_dist     -f    complex.gro    -s   g-dist.tpr    -o  g-dist.xvg
>>
>>        but the result was an empty g-dist.xvg and:
>>
>>        Fatal error:
>>        Unexpected end of file in file   631LIG  C12     45  -0.475
>>         -0.514  -0.434 at line 2
>>        (Source file ../../../../src/gmxlib/confio.
>>        c, line 725)
>>
>>
>>    How many atoms are in complex.gro?  To what line number does this
>>    atom entry correspond?  It seems g_dist thinks the file should end
>>    here, prematurely.
>>
>>    -Justin
>>
>>
>>        besides,I want to measure this distance befor erunning and as a
>>        vector.
>>        below is a part of my complex.gro:
>>         631LIG  F1      42  -0.701  -0.571  -0.151
>>         631LIG  C16     43  -0.534  -0.501  -0.306
>>         631LIG  H16     44  -0.491  -0.434  -0.232
>>         631LIG  C12     45  -0.475  -0.514  -0.434
>>         631LIG  H12     46  -0.394  -0.446  -0.459
>>
>>
>>        thanks in advances
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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