[gmx-users] g-dist

[Justin A. Lemkul]

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

========================================