[gmx-users] g-dist
Justin A. Lemkul
jalemkul at vt.edu
Tue Dec 21 14:56:04 CET 2010
mohsen ramezanpour wrote:
> Dear Justin
>
> WARNING 1 [file g-dist.mdp, line unknown]:
> Can only use nstype=Simple with pbc=no, setting nstype to Simple
> WARNING 2 [file complex.top, line 39718]:
> Bad box in file complex.gro
>
> Generated a cubic box 10.816 x 14.959 x 9.086
> Warning: atom name 6439 in complex.top and complex.gro does not match
> (C18 - H9N)
> Warning: atom name 6440 in complex.top and complex.gro does not match
> (C6 - H9O)
> Warning: atom name 6441 in complex.top and complex.gro does not match
> (C11 - H19)
> Warning: atom name 6442 in complex.top and complex.gro does not match
> (H11 - C18)
> Warning: atom name 6443 in complex.top and complex.gro does not match
> (C15 - C6)
> Warning: atom name 6444 in complex.top and complex.gro does not match
> (H15 - C11)
> Warning: atom name 6445 in complex.top and complex.gro does not match
> (C17 - H11)
> Warning: atom name 6446 in complex.top and complex.gro does not match
> (F1 - C15)
> Warning: atom name 6447 in complex.top and complex.gro does not match
> (C16 - H15)
> Warning: atom name 6448 in complex.top and complex.gro does not match
> (H16 - C17)
> Warning: atom name 6449 in complex.top and complex.gro does not match
> (C12 - F1)
> Warning: atom name 6450 in complex.top and complex.gro does not match
> (H12 - C16)
>
> WARNING 3 [file complex.top, line 39718]:
> 12 non-matching atom names
> atom names from complex.top will be used
> atom names from complex.gro will be ignored
These are very important warnings, and hence why I said one should never blindly
use -maxwarn unless you fully understand their implications. The order of the
contents of the coordinate file must match the order of the moleculetypes listed
in the [molecules] directive of the topology, and the order of the underlying
topologies must match. You've got a bunch of mismatches here, indicating that
at least one of these criteria is not satisfied, so anything you do (be it
simulation or analysis) will be complete garbage.
Fix your coordinate file and try again. Don't use -maxwarn. If grompp fails,
it's for a reason.
-Justin
>
> besides I generated it as enzyme/drug tutorial.
> besides C12 is in line 2 from the end of the page.
> thanks in advance
>
>
>
>
>
> On Tue, Dec 21, 2010 at 5:11 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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> <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 <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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