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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