On 12/20/13 2:20 PM, Sidath Wijesinghe wrote:
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?
No. If that's actually the entirety of the topology, it basically contains
nothing. You're missing 99.9% of the required information.
-Justin
Thank you!
On Thu, Dec 19, 2013 at 8:01 AM, Justin Lemkul <jalem...@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 <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
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==================================================
Justin A. Lemkul, Ph.D.
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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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send a mail to gmx-users-requ...@gromacs.org.
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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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