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 <jalem...@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 <jalem...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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