[gmx-users] g-dist

[mohsen ramezanpour]

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.

besides it is in 6454 line of complex.gro






On Tue, Dec 21, 2010 at 4:32 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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