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
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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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