[gmx-users] g-dist

[Justin A. Lemkul]

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
> 

-- 
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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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