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 <[email protected]
<mailto:[email protected]>> 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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