[gmx-users] g-dist
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Wed Dec 22 09:50:26 CET 2010
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?
Where is my mistake?
ُthanks in advanvce
On Tue, Dec 21, 2010 at 5:26 PM, Justin A. Lemkul <jalemkul at 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 <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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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