Dear justin <br>please check this part of my .gro file.<br> ...<br> 630VAL C 6416 0.554 11.700 -0.442<br> 630VAL O1 6417 0.522 11.605 -0.534<br> 630VAL O2 6418 0.534 11.834 -0.454<br> 631<1> N2 1 2.686 2.399 2.151<br>
631<1> C20 2 2.613 2.375 2.230<br> 631<1> C14 3 2.519 2.345 2.331<br> 631<1> C10 4 2.464 2.452 2.405<br> ...<br>I used the prodrg server and edited my protein.gro file.<br>
Is this correct?<br>Where is my mistake?<br>ُthanks in advanvce<br><br><br><br><br><br><br><br><br><div class="gmail_quote">On Tue, Dec 21, 2010 at 5:26 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin<br>
<br>
WARNING 1 [file g-dist.mdp, line unknown]:<br>
Can only use nstype=Simple with pbc=no, setting nstype to Simple<br>
WARNING 2 [file complex.top, line 39718]:<br>
Bad box in file complex.gro<br>
<br>
Generated a cubic box 10.816 x 14.959 x 9.086<br>
Warning: atom name 6439 in complex.top and complex.gro does not match (C18 - H9N)<br>
Warning: atom name 6440 in complex.top and complex.gro does not match (C6 - H9O)<br>
Warning: atom name 6441 in complex.top and complex.gro does not match (C11 - H19)<br>
Warning: atom name 6442 in complex.top and complex.gro does not match (H11 - C18)<br>
Warning: atom name 6443 in complex.top and complex.gro does not match (C15 - C6)<br>
Warning: atom name 6444 in complex.top and complex.gro does not match (H15 - C11)<br>
Warning: atom name 6445 in complex.top and complex.gro does not match (C17 - H11)<br>
Warning: atom name 6446 in complex.top and complex.gro does not match (F1 - C15)<br>
Warning: atom name 6447 in complex.top and complex.gro does not match (C16 - H15)<br>
Warning: atom name 6448 in complex.top and complex.gro does not match (H16 - C17)<br>
Warning: atom name 6449 in complex.top and complex.gro does not match (C12 - F1)<br>
Warning: atom name 6450 in complex.top and complex.gro does not match (H12 - C16)<br>
<br>
WARNING 3 [file complex.top, line 39718]:<br>
12 non-matching atom names<br>
atom names from complex.top will be used<br>
atom names from complex.gro will be ignored<br>
</blockquote>
<br></div>
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.<br>
<br>
Fix your coordinate file and try again. Don't use -maxwarn. If grompp fails, it's for a reason.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
besides I generated it as enzyme/drug tutorial.<br>
besides C12 is in line 2 from the end of the page.<br>
thanks in advance<br>
<br>
<br>
<br>
<br>
<br></div><div><div></div><div class="h5">
On Tue, Dec 21, 2010 at 5:11 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
<br>
Dear justin<br>
after using grompp without -maxwarn I faced these:<br>
<br>
NOTE 2 [file g-dist.mdp, line unknown]:<br>
You are using a plain Coulomb cut-off, which might produce<br>
artifacts.<br>
You might want to consider using PME electrostatics.<br>
<br>
<br>
This run will generate roughly 2 Mb of data<br>
writing run input file...<br>
<br>
There were 2 notes<br>
<br>
There were 3 warnings<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.7<br>
Source code file: ../../../../src/gmxlib/gmx_fatal.c, line: 481<br>
<br>
Fatal error:<br>
Too many warnings (3), grompp terminated.<br>
If you are sure all warnings are harmless, use the -maxwarn option.<br>
<br>
<br>
None of this output actually indicates what the errors are. I don't<br>
know if any of it will be relevant to the problem at hand, but<br>
without seeing what the errors are, there's no way to rule out<br>
incorrect input.<br>
<br>
<br>
besides it is in 6454 line of complex.gro<br>
<br>
<br>
How did you generate complex.gro? If it is line 6454, it is not<br>
numbered accordingly. That doesn't matter, in theory, but if you've<br>
just simply concatenated the protein and ligand coordinate files and<br>
left any extraneous information in the .gro file, it could be<br>
causing the error.<br>
<br>
-Justin<br>
<br>
<br>
<br>
<br>
<br>
<br>
On Tue, Dec 21, 2010 at 4:32 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
<br>
Dear All<br>
I did the Enzyme/drug tutorial and generated complex.gro and<br>
complex.top files as was said.<br>
Now I want to measure the distance between center of mass of<br>
protein and drug<br>
I used g_dist but I could not.<br>
I entered these commands(of course I made an index.ndx and<br>
g-dist.tpr):<br>
<br>
I used from an typical .mdp file to generate .tpr file by<br>
below<br>
command:<br>
<br>
grompp -c complex.gro -p complex.top -o<br>
g-dist.tpr -f g-dist.mdp -maxwarn 3<br>
<br>
<br>
What warnings are you ignoring? This is, in general, a very<br>
bad idea.<br>
<br>
<br>
then,<br>
g_dist -f complex.gro -s g-dist.tpr -o<br>
g-dist.xvg<br>
<br>
but the result was an empty g-dist.xvg and:<br>
<br>
Fatal error:<br>
Unexpected end of file in file 631LIG C12 45 -0.475<br>
-0.514 -0.434 at line 2<br>
(Source file ../../../../src/gmxlib/confio.<br>
c, line 725)<br>
<br>
<br>
How many atoms are in complex.gro? To what line number does this<br>
atom entry correspond? It seems g_dist thinks the file<br>
should end<br>
here, prematurely.<br>
<br>
-Justin<br>
<br>
<br>
besides,I want to measure this distance befor erunning<br>
and as a<br>
vector.<br>
below is a part of my complex.gro:<br>
631LIG F1 42 -0.701 -0.571 -0.151<br>
631LIG C16 43 -0.534 -0.501 -0.306<br>
631LIG H16 44 -0.491 -0.434 -0.232<br>
631LIG C12 45 -0.475 -0.514 -0.434<br>
631LIG H12 46 -0.394 -0.446 -0.459<br>
<br>
<br>
thanks in advances<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
<br>
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<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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