[gmx-users] Error in system_inflate.gro coordinates does not match

[Justin Lemkul]

On 7/21/14, 11:30 AM, RINU KHATTRI wrote:
> hello everyone
> thanks justin it works but problem is at the same place even one more
> problem ligand is out side the protein and protein is out side the popc

So you've placed the ligand incorrectly or otherwise manipulated the coordinates 
wrong.  Given the absence of any other information, it's impossible to suggest 
anything.

-Justin

> kindly help
>
>
> On Sat, Jul 19, 2014 at 7:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/19/14, 9:56 AM, RINU KHATTRI wrote:
>>
>>> hello everyone
>>>
>>> i know justin -D is for minim.mdp not for topology i used simply D
>>>
>>
>> That's still wrong.  There should be no "D" or "-D" in the #ifdef
>> statement; it's cpp macro syntax.  Please look at the block I provided
>> before:
>>
>>
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>> Use it exactly.  Copy and paste it.  Invoke it with "define =
>> -DSTRONG_POSRES"
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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