mohsen ramezanpour wrote:
Dear justin
please check this part of my .gro file.
...
630VAL C 6416 0.554 11.700 -0.442
630VAL O1 6417 0.522 11.605 -0.534
630VAL O2 6418 0.534 11.834 -0.454
631<1> N2 1 2.686 2.399 2.151
631<1> C20 2 2.613 2.375 2.230
631<1> C14 3 2.519 2.345 2.331
631<1> C10 4 2.464 2.452 2.405
...
I used the prodrg server and edited my protein.gro file.
Is this correct?
Clearly not, or you wouldn't have an error.
Where is my mistake?
Based on what I see above, there is something weird in the residue name, but it
doesn't correspond to what you've posted previously, so I don't know what to
believe. The atom name column is misaligned, but I don't know if that will
cause a problem.
Combining the .gro files is very easy:
1. cat protein.gro drg.gro > complex.gro
2. Remove the unnecessary box vectors, title line, and atom count in the middle
of the file.
3. Increment the number of atoms on the second line of complex.gro to reflect
the proper number of atoms.
All of that assumes, of course, that both the protein and ligand are in the same
box, such that the box vectors at the end of drg.gro are applicable to the
protein, as well.
-Justin
ُthanks in advanvce
On Tue, Dec 21, 2010 at 5:26 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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>
<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> <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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