[gmx-users] OPLS force field issue....

Sidath Wijesinghe swijesi at g.clemson.edu
Fri Dec 20 20:20:17 CET 2013


Justin,

i went for the option 4 that u pointed out. let me explain what i did,

i converted the .pdb file in to .gro by using.

editconf -f test.pdb -o test.gro -box 18 18 18 -angles 90 90 90

then i use the text editor as follows.


Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/ions.itp"
[ moleculetype ]
; name  nrexcl
  UNK     3

then i did

 grompp -f npt.mdp -c test.gro -p test.top -o run.tpr

and i got following error...

Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 479

Fatal error:
No molecules were defined in the system

could you please help me out here? am i doing it correct?

Thank you!


On Thu, Dec 19, 2013 at 8:01 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/18/13 10:13 PM, Sidath Wijesinghe wrote:
>
>> could you please give me a hint about a suitable method for this task?
>>
>>
> You can make just about anything work.
>
> 1. pdb2gmx with .rtp entries for each of your molecules, with
> appropriately named (unique) atoms
> 2. g_x2top can also process each different molecule type, yielding
> topologies for each of them individually.  Conversion from .top to .itp is
> trivial.
> 3. Software of your own creation
> 4. Chapter 5 of the manual and your favorite text editor (laborious, but
> works well if you know what you are doing)
>
> -Justin
>
>
>  thank you!
>>
>>
>> On Wed, Dec 18, 2013 at 9:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 12/18/13 9:46 PM, Sidath Wijesinghe wrote:
>>>
>>>     Is g_x2top  the only way for my situation? or am i in the wrong
>>>> track?
>>>>
>>>>
>>>>  There are numerous ways to generate topologies.  I have warned you that
>>> g_x2top is probably ill-suited for this task.  It works well for simple
>>> things.  It does not work well for complex systems.
>>>
>>>
>>>   if i find the parameters for the missing parameters how can i get rid
>>> of
>>>
>>>> sodium as u mentioned
>>>> for the real system with Na+ ions?
>>>>
>>>>
>>>>  I answered this question in my previous message.
>>>
>>> -Justin
>>>
>>>
>>>   Thank you!
>>>
>>>>
>>>>
>>>> On Wed, Dec 18, 2013 at 9:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 12/18/13 9:32 PM, Sidath Wijesinghe wrote:
>>>>>
>>>>>   Justin,
>>>>>
>>>>>>
>>>>>> As i understood from reading and tutorial what i should do is, lets
>>>>>> say
>>>>>> i
>>>>>> generated a topology file named as
>>>>>> topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it
>>>>>> accounts
>>>>>> for Na+.
>>>>>>
>>>>>> my question is..
>>>>>>
>>>>>> 1.how can i get rid of sodium? just removing the corresponding lines
>>>>>> from
>>>>>> the .pdb text?
>>>>>>
>>>>>>
>>>>>>  Yes, for the coordinate file processed by g_x2top.  Once the
>>>>> topology for
>>>>> everything else is established and you have #included the topology for
>>>>> sodium (as I explained before), you can use the original coordinate
>>>>> file.
>>>>>
>>>>>
>>>>>    2. i tried with uncharged system for simplicity with less number of
>>>>>
>>>>>  atoms..(
>>>>>> here i replaced the COONa functional group with a CH3 group)
>>>>>>
>>>>>> but still g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc
>>>>>>
>>>>>> am getting this parameters missing..
>>>>>>
>>>>>> Can not find forcefield for atom C-147 with 1 bonds
>>>>>> Can not find forcefield for atom C-148 with 1 bonds
>>>>>> Can not find forcefield for atom C-873 with 1 bonds
>>>>>> Can not find forcefield for atom C-874 with 1 bonds
>>>>>> Can not find forcefield for atom C-939 with 1 bonds
>>>>>> Can not find forcefield for atom C-940 with 1 bonds
>>>>>> Can not find forcefield for atom C-1137 with 1 bonds
>>>>>> Can not find forcefield for atom C-1138 with 1 bonds
>>>>>> Can not find forcefield for atom C-1269 with 1 bonds
>>>>>> Can not find forcefield for atom C-1270 with 1 bonds
>>>>>>
>>>>>> for that do i need to modify the atomname2type.n2t  the way i did
>>>>>> earlier?or am i doing this wrong?
>>>>>>
>>>>>>
>>>>>>   g_x2top is not very smart.  You have to give it all the information
>>>>>>
>>>>> needed
>>>>> for it to work.  Whenever you get this error, the solution is always
>>>>> the
>>>>> same - those atoms are not accounted for by whatever is in the .n2t
>>>>> file,
>>>>> so you need to add information to cover those atoms.
>>>>>
>>>>> -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 | (410) 706-7441
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>  --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> 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
>
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>



-- 
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University


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