[gmx-users] Problem using gromacs

[Justin Lemkul]

On 1/4/16 8:20 AM, masoud keramati wrote:
> in OPLS ff when i use tip3p  water  i got this error but if tip3p selected
> then there no problem and it's interesting!
>

This comment makes no sense.  Changing water models (presumably that is what you 
mean, and just typoed it) will not work unless you re-solvate the system. 
TIP3P, TIP4P, and TIP5P all have different numbers of atoms, hence there will 
certainly be a mismatch with the topology if you simply try to change the water 
model when running genbox.

-Justin

> On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/4/16 4:27 AM, soumi  wrote:
>>
>>> Respected Sir,
>>>                 I am new user of gromacs. When I use the following command
>>> gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr
>>>
>>> I get the following error :Number of coordinates in coordinate file does
>>> not match topology file.
>>> Please tell me how can I correct the number of coordinates in gromacs?
>>>
>>>
>>
>> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>>
>> Since you've (presumably) already solvated the system, you probably forgot
>> to let genbox adjust your topology for you via the -p option.  Based on
>> your file naming, I assume you're following my lysozyme tutorial, which
>> lays everything out exactly, so be sure you're using the exact commands and
>> you know what each option is doing.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>>
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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

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