Re: [gmx-users] PROBLEM IN COORDINATES

[neelam wafa]

thanks. problem resolved.

On 21 Feb 2018 08:13, "Justin Lemkul"  wrote:

>
>
> On 2/20/18 9:50 PM, neelam wafa wrote:
>
>> Dear gmx users
>>
>> I am still stuck at this point.
>> error obtained is this
>> Fatal error:
>> number of coordinates in coordinate file (solv.gro, 32803)
>>   does not match topology (topol.top, 32818)
>> There is a difference of 15. I think its not considering the ligand as 15
>> is i think for ligand. the ligand. the entries of ligand in gro file are
>> these.
>> 15
>>  1JZ4  C4   1   2.946  -2.601   0.141
>>  1JZ4  C14  2   3.009  -2.568   0.005
>>  1JZ4  C13  3   2.965  -2.664  -0.107
>>  1JZ4  C12  4   2.834  -2.642  -0.154
>>  1JZ4  C11  5   2.734  -2.734  -0.116
>>  1JZ4  H11  6   2.753  -2.810  -0.040
>>  1JZ4  C7   7   2.606  -2.727  -0.176
>>  1JZ4  H7   8   2.529  -2.798  -0.147
>>  1JZ4  C8   9   2.578  -2.628  -0.273
>>  1JZ4  H8  10   2.479  -2.624  -0.319
>>  1JZ4  C9  11   2.677  -2.536  -0.311
>>  1JZ4  H9  12   2.655  -2.460  -0.387
>>  1JZ4  C10 13   2.804  -2.543  -0.251
>>  1JZ4  OAB 14   2.900  -2.451  -0.285
>>  1JZ4  HAB 15   2.863  -2.389  -0.354
>> 0.68000   0.68000   0.68000
>>
>> Help me out please.
>>
>
> Looks like you probably didn't copy the ligand coordinates into the
> topology. The topology thinks it's there and the coordinates say it's not.
> The solution to this error is always the same: proper bookkeeping.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] PROBLEM IN COORDINATES

[Justin Lemkul]

On 2/20/18 9:50 PM, neelam wafa wrote:

Dear gmx users

I am still stuck at this point.
error obtained is this
Fatal error:
number of coordinates in coordinate file (solv.gro, 32803)
  does not match topology (topol.top, 32818)
There is a difference of 15. I think its not considering the ligand as 15
is i think for ligand. the ligand. the entries of ligand in gro file are
these.
15
 1JZ4  C4   1   2.946  -2.601   0.141
 1JZ4  C14  2   3.009  -2.568   0.005
 1JZ4  C13  3   2.965  -2.664  -0.107
 1JZ4  C12  4   2.834  -2.642  -0.154
 1JZ4  C11  5   2.734  -2.734  -0.116
 1JZ4  H11  6   2.753  -2.810  -0.040
 1JZ4  C7   7   2.606  -2.727  -0.176
 1JZ4  H7   8   2.529  -2.798  -0.147
 1JZ4  C8   9   2.578  -2.628  -0.273
 1JZ4  H8  10   2.479  -2.624  -0.319
 1JZ4  C9  11   2.677  -2.536  -0.311
 1JZ4  H9  12   2.655  -2.460  -0.387
 1JZ4  C10 13   2.804  -2.543  -0.251
 1JZ4  OAB 14   2.900  -2.451  -0.285
 1JZ4  HAB 15   2.863  -2.389  -0.354
0.68000   0.68000   0.68000

Help me out please.


Looks like you probably didn't copy the ligand coordinates into the 
topology. The topology thinks it's there and the coordinates say it's 
not. The solution to this error is always the same: proper bookkeeping.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] PROBLEM IN COORDINATES

[neelam wafa]

Dear gmx users

I am still stuck at this point.
error obtained is this
Fatal error:
number of coordinates in coordinate file (solv.gro, 32803)
 does not match topology (topol.top, 32818)
There is a difference of 15. I think its not considering the ligand as 15
is i think for ligand. the ligand. the entries of ligand in gro file are
these.
15
1JZ4  C4   1   2.946  -2.601   0.141
1JZ4  C14  2   3.009  -2.568   0.005
1JZ4  C13  3   2.965  -2.664  -0.107
1JZ4  C12  4   2.834  -2.642  -0.154
1JZ4  C11  5   2.734  -2.734  -0.116
1JZ4  H11  6   2.753  -2.810  -0.040
1JZ4  C7   7   2.606  -2.727  -0.176
1JZ4  H7   8   2.529  -2.798  -0.147
1JZ4  C8   9   2.578  -2.628  -0.273
1JZ4  H8  10   2.479  -2.624  -0.319
1JZ4  C9  11   2.677  -2.536  -0.311
1JZ4  H9  12   2.655  -2.460  -0.387
1JZ4  C10 13   2.804  -2.543  -0.251
1JZ4  OAB 14   2.900  -2.451  -0.285
1JZ4  HAB 15   2.863  -2.389  -0.354
   0.68000   0.68000   0.68000

Help me out please.

Regards

On Sun, Feb 18, 2018 at 6:45 PM, Alex  wrote:

> Hi,
>
> The error is informative. Check the number of entries in the gro file and
> compare it with the [ atoms ] section in your topology, together with
> anything that's added under [ system ]. The total numbers need to match.
>
> Alex
>
>
>
> On 2/18/2018 11:34 AM, neelam wafa wrote:
>
>> Dear gmx users,
>>
>> I am doing the tutorial of protein ligand simmulation given at
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/com.
>> when I give following command, I get an error.
>>
>> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>
>> the error says the number of coordinates in the sol.gro file and
>> topol.top file does not match. How to fix it.
>>
>> Help me out please.
>>
>> Thanks in advance.
>>
>> Regards
>>
>
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Re: [gmx-users] PROBLEM IN COORDINATES

[Alex]

Hi,

The error is informative. Check the number of entries in the gro file 
and compare it with the [ atoms ] section in your topology, together 
with anything that's added under [ system ]. The total numbers need to 
match.


Alex


On 2/18/2018 11:34 AM, neelam wafa wrote:

Dear gmx users,

I am doing the tutorial of protein ligand simmulation given at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com.
when I give following command, I get an error.

gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

the error says the number of coordinates in the sol.gro file and
topol.top file does not match. How to fix it.

Help me out please.

Thanks in advance.

Regards


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Re: [gmx-users] PROBLEM IN COORDINATES

[Ali Ahmed]

check your sol.gro if you have molecules more or less than given in your
topology
Best

On Sun, Feb 18, 2018 at 12:34 PM, neelam wafa  wrote:

> Dear gmx users,
>
> I am doing the tutorial of protein ligand simmulation given at
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com
> .
> when I give following command, I get an error.
>
> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>
> the error says the number of coordinates in the sol.gro file and
> topol.top file does not match. How to fix it.
>
> Help me out please.
>
> Thanks in advance.
>
> Regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] PROBLEM IN COORDINATES

[neelam wafa]

Dear gmx users,

I am doing the tutorial of protein ligand simmulation given at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com.
when I give following command, I get an error.

gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

the error says the number of coordinates in the sol.gro file and
topol.top file does not match. How to fix it.

Help me out please.

Thanks in advance.

Regards
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