Re: [gmx-users] g-dist

[Tsjerk Wassenaar]

Hi Mohsen,

I think you'll have to get a bit creative with g_traj to get the COMs,
followed by either some simple scripting or nifty usage of paste and awk
(something like: paste com1.xvg com2.xvg | awk '/^...@#;]/{print $2-$6,
$3-$7, $4-$8}').

Hope it helps,

Tsjerk

On Dec 25, 2010 2:40 PM, "mohsen ramezanpour" 
wrote:

Dear All
How can we measure the distance between COM of two molecules?of course in
vector form!
thanks in advance

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[gmx-users] g-dist

[mohsen ramezanpour]

Dear All
How can we measure the distance between COM of two molecules?of course in
vector form!
thanks in advance
-- 
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Please search the archive at 
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Re: [gmx-users] g-dist

[Justin A. Lemkul]

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 > 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 x9.086
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
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 

Re: [gmx-users] g-dist

[mohsen ramezanpour]

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  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 x9.086
>> 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>> 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
>>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.
>>   

Re: [gmx-users] g-dist

[Justin A. Lemkul]

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 x9.086
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 > 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
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 -fg-dist.mdp-maxwarn 3


   What warnings are you ignoring?  This is, in general, a very
bad idea.


   then,
   g_dist -fcomplex.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

Re: [gmx-users] g-dist

[mohsen ramezanpour]

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 x9.086
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

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  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>> 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
>>   -fg-dist.mdp-maxwarn 3
>>
>>
>>What warnings are you ignoring?  This is, in general, a very bad idea.
>>
>>
>>then,
>>g_dist -fcomplex.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  | (540) 231-9080
>>
>>http://www.bevanlab.bioc

Re: [gmx-users] g-dist

[Justin A. Lemkul]

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 > 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
 -fg-dist.mdp-maxwarn 3



What warnings are you ignoring?  This is, in general, a very bad idea.


then,
g_dist -fcomplex.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  | (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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Re: [gmx-users] g-dist

[mohsen ramezanpour]

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.

besides it is in 6454 line of complex.gro






On Tue, Dec 21, 2010 at 4:32 PM, Justin A. Lemkul  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 -fcomplex.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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@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!
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Re: [gmx-users] g-dist

[Justin A. Lemkul]

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  
-fg-dist.mdp-maxwarn 3


What warnings are you ignoring?  This is, in general, a very bad idea.


then,
g_dist -fcomplex.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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g-dist

[mohsen ramezanpour]

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
then,
g_dist -fcomplex.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)

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
-- 
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