[gmx-users] [gmx-user] coordinates mismatch error

[Justin Lemkul]

On 12/31/19 9:43 AM, Quin K wrote:
> Could it be due to protein-ligand complex being at the edge of the box?
> https://drive.google.com/file/d/187fPACfq1QybNJxkyJKB8faUPOBRFccK/view?usp=sharing

Your link requires permission to view, but in any case, no, this has 
nothing to do with the error.

The solution to this error is always the same - proper bookkeeping. You 
have a difference of 69 atoms that are in the coordinates but not the 
topology. How many atoms are in your ligand? Do you have the right 
number of water molecules specified?

-Justin

>
>
> On Tue, Dec 31, 2019 at 8:06 PM Quin K <profiles.ke at gmail.com> wrote:
>
>> Hi
>>
>> I continue to get following error during complex MD
>>
>>
>>
>> *number of coordinates in coordinate file (solv.gro, 50670)does not match
>> topology (topol.top, 50701)*
>> I don't understand why there's a mismatch.
>> I followed the instructions in mdtutorials.com for Gromacs ligand-protien
>> complex.
>>
>> How can I rectify this?
>>
>> Regards
>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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