[gmx-users] question

[RAHUL SURESH]

On Sat, 30 Dec 2017 at 12:10 PM, s.ghasemlou <s.ghasemlou at ut.ac.ir> wrote:

> Hello every one,
>
> After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
> topol.top -o ions.tpr" I get the error:
>
> ERROR 1 [file topol.top, line 863]:
>   ERROR: The cut-off length is longer than half the shortest box vector
> or
>   longer than the smallest box diagonal element. Increase the box size
> or
>   decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343)

What is the cut off scheme and value..?

>
>
> I have tried different rlist, r columb and rvdw values. I have also
> changed the box vector several times, but I still get the same error. I
> don't know how to change them to fix the error.
>
> There is also the below warning:
>
> Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
> - OW)
> Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
> HW1)
> Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
> - HW2)
> Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
> - OW)
> Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
> HW1)
> Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
> - HW2)
> Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
> - OW)
> Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
> - HW1)
> Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
> - HW2)
> Warning: atom name 10 in topol.top and totalbox1.gro does not match
> (H110 - OW)
> Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
> - HW1)
> Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
> - HW2)
> Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
> - OW)
> Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
> - HW1)
> Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
> - HW2)
> Warning: atom name 16 in topol.top and totalbox1.gro does not match
> (H100 - OW)
> Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
> - HW1)
> Warning: atom name 18 in topol.top and totalbox1.gro does not match
> (H102 - HW2)
> Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
> - OW)
> Warning: atom name 20 in topol.top and totalbox1.gro does not match
> (H101 - HW1)
> (more than 20 non-matching atom names)
> WARNING 1 [file topol.top, line 863]:
>   32798 non-matching atom names
>   atom names from topol.top will be used
>   atom names from totalbox1.gro will be ignored

You can use maxwarn flag.... or change the cane in toolbox.gro

>
>
> As I checked both the .gro and topol.top contents, atom names are the
> same but here atom names of solvent water are mixed with atom names of
> the ligand I used.

Someone else would definitely help you in This.

>
> please help me on this. Thanks in advance.
> --
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*