[gmx-users] error running grompp for ions.mdp input

[Justin Lemkul]

On 2/16/16 10:04 AM, Ghada Mhmd wrote:
> I'm still getting the same error but with different numbers even though I
> calculated the number of molecules of each [Moleculetype] in the .gro file
> and changed the number accordingly
>

Then whatever you calculated was incorrect.  A mismatch here is a very simple 
issue of bookkeeping.

-Justin

> On Tue, Feb 16, 2016 at 4:26 PM, Smith, Micholas D. <smithmd at ornl.gov>
> wrote:
>
>> At the end of your topology file, make sure you have the correct number of
>> molecules of each type
>> (typically the end of the .top file will look something like:
>>
>> [ molecules ]
>> Protein    1    ;Number of proteins
>> SOL        59990 ;Number of waters
>> Na           2 ; Number of Na ions
>> Cl            2; Number of Cl ions
>>
>> In your case you should have something like:
>>
>> [ molecules ]
>> Protein       1 ;Number of proteins
>> MET         (); Number of Methanol Molecules
>> SOL         (); Number of Solvent molecules
>>
>>
>> ===================
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Ghada
>> Mhmd <ghada.mhmd22 at gmail.com>
>> Sent: Tuesday, February 16, 2016 8:19 AM
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: [gmx-users] error running grompp for ions.mdp input
>>
>> hello
>>
>> I'm new to gromacs I'm simulating a protein in a mixed solvent
>> (water/organic solvent)
>>
>> *first I added my organic solvent molecule (Methanol) using gmx
>> insert-molecules command
>>
>> *then I solvate it in water using gmx solvate command
>>
>> but I went to adding atom using gmx grompp command
>>
>>
>>
>>
>>
>>
>>
>> *I get this error : Fatal error: number of coordinates in coordinate file
>> (3im_solv.gro, 161232)              does not match topology (topol.top,
>> 492074) For more information and tips for troubleshooting, please check the
>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>> <http://www.gromacs.org/Documentation/Errors> *I don't know which changes
>> I
>> need to apply on the topology.top file to get it updated
>> I tried to change the numbers in the .top file to match the number given at
>> the top of the coordinate 3im_solv.gro file but I still get the same error
>> but with different numbers.
>>
>>
>> * any help would be appreciated  *thanks
>> Ghada
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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

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