[gmx-users] fatal erroe in prorein-ligand comlex

[Justin Lemkul]

On 12/16/14 9:11 PM, Bikash Ranjan Sahoo wrote:
> Dear Yaser,
> Gro file is sensitive and you should update the number manually after
> adding the ligand atoms to the protein.gro file. Check the first line of
> your protein.gro and ligand.gro. In the complex.gro the first line should
> be the summation of both. Gromacs does not perform it manually. Kindly chck
> again and rerun the grompp.
>

Incorrect formatting or contents of the .gro file should not trigger this fatal 
error; there are other error messages if there are too many or too few atoms in 
the .gro file.

-Justin

>
> Good luck
> Bikash
> Osaka
>
> On Wednesday, December 17, 2014, Yaser Hosseini <
> yaser.hosseini.biologist at gmail.com> wrote:
>
>> hi gromacs users
>>
>> i got error in step four in protein-ligand complex how can i fix it:
>>
>> Fatal error:
>> number of coordinates in coordinate file (solv.gro, 144131)
>>               does not match topology (topol.top, 144171)
>>
>> when i want to ran this:
>>
>> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>
>> i add my ligand drg.gro in protein_processed.gro.
>>
>> beside i cant find conf.gro that you say in this toturial:
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html
>>
>> thank you .
>> --
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>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================