[gmx-users] NMR restrained MD

Justin Lemkul jalemkul at vt.edu
Tue Sep 10 15:25:51 CEST 2013



On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
> Hi Justin,
>
> This is another type of error while running energy minimization:
> what to do for these type of errors.
>

They're exactly the same as the dihedral error from before.  You're using 
parameters that don't exist in the force field.

-Justin

> ERROR 218 [file topol.top, line 23487]:
>    No default Ryckaert-Bell. types
>
>
> ERROR 219 [file topol.top, line 23499]:
>    No default Ryckaert-Bell. types
>
>
> ERROR 220 [file topol.top, line 23500]:
>    No default Ryckaert-Bell. types
>
>
> ERROR 221 [file topol.top, line 23501]:
>    No default Ryckaert-Bell. types
>
>
> ERROR 222 [file topol.top, line 23502]:
>    No default Ryckaert-Bell. types
>
>
> ERROR 223 [file topol.top, line 23503]:
>    No default Ryckaert-Bell. types
>
>
> ERROR 224 [file topol.top, line 23515]:
>    No default Ryckaert-Bell. types
>
>
> --Rama
>
>
> On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote:
>>
>>> Hi Justin,
>>>
>>> I included 1 DMPC molecule parameters in the file should I need to include
>>> 128 molecules parameters in the file .rtp.
>>>
>>>
>> No.  Residue definitions are used any time they are encountered in the
>> coordinate file.  There is no need for such redundancy at the force field
>> level.
>>
>>
>> -Justin
>>
>> --
>> ==============================**====================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
>> 706-7441
>>
>> ==============================**====================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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



More information about the gromacs.org_gmx-users mailing list