Dear Chansoo Kim,
It has passed relatively long time since I attempted to use pdb2gmx to
build my topology for polyethylene. I prepared the relevant files
according to those used for amino acids. I used + and – sign to discern
the direction of connectivity. I have encountered dome problems
mentioned in the mail but they have not been answered satisfactorily.
Later on I wanted to run just united atom simulations and I had next
problem with pdb2gmx that always include hydrogen atoms to my topology
though I used option which should have disabled this. I decided to build
my topology file without pdb2gmx and I applied force field that is not
present in GMX directories.
------------------------------------------------------------------------
*From:* gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Chansoo Kim
*Sent:* Tuesday, March 03, 2009 2:50 PM
*To:* jalem...@vt.edu; Discussion list for GROMACS users
*Subject:* Re: [gmx-users] Polyethylene (PE) simulations in Gromacs -
please!
Dear Justin:
Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.
I totally understand how topology files (tdb, hdb, and etc..) work, but
I do not clearly understand chemical reaction, which I have to define in
those files...
*[Situation]*
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...
*[Topology files and etc]*
(1) rtp file
[ Eth ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
[ bonds ]
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 +C1
(2) hdb file
Eth 2
2 6 H1 C1 C2 +C1
2 6 H2 C2 C1 -C2
(3) -c.tdb file
[ Eth ]
[ replace ]
C1 opls_135 12.011 -0.18
[ add ]
3 4 H1 C1 C2
opls_140 1.008 0.06
[ delete ]
H21
H22
(4) -n.tdb file
[ Eth ]
[ replace ]
C2 opls_135 12.011 -0.18
[ add ]
3 4 H2 C2 C1
opls_140 1.008 0.06
[ delete ]
H21
H22
(5) input pdb file
ATOM 1 C1 Eth 1 1.000 1.540 0.000
ATOM 2 C2 Eth 1 2.456 2.041 0.000
ATOM 3 C1 Eth 2 2.456 3.581 0.000
ATOM 4 C2 Eth 2 3.912 4.083 0.000
ATOM 5 C1 Eth 3 3.912 5.623 0.000
ATOM 6 C2 Eth 3 5.368 6.124 0.000
END
*[Error]*
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"
*[Question #1 and #2]*
Therefore, what I should define more...?
What does the "+" and "-" mean here?
*[If...]*
If I change the hdb file as follows,
Eth 2
2 6 H1 C1 C2 C1
2 6 H2 C2 C1 C2
After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did
NOT work...).
And those positions are all (0, 0, 0).
Following is the results,
LE Giving Russians Opium May Alter Current Situation
MODEL 1
ATOM 1 C1 PEt 1 1.000 0.000 0.000 1.00 0.00
ATOM 2 H11 PEt 1 0.000 0.000 0.000 1.00 0.00
ATOM 3 H12 PEt 1 0.000 0.000 0.000 1.00 0.00
ATOM 4 C2 PEt 1 2.450 6.000 1.000 1.00 0.00
ATOM 5 H21 PEt 1 0.000 0.000 0.000 1.00 0.00
ATOM 6 H22 PEt 1 0.000 0.000 0.000 1.00 0.00
ATOM 7 C1 PEt 2 2.450 6.000 1.000 1.00 0.00
ATOM 8 H11 PEt 2 0.000 0.000 0.000 1.00 0.00
ATOM 9 H12 PEt 2 0.000 0.000 0.000 1.00 0.00
ATOM 10 C2 PEt 2 3.910 2.000 3.000 1.00 0.00
ATOM 11 H21 PEt 2 0.000 0.000 0.000 1.00 0.00
ATOM 12 H22 PEt 2 0.000 0.000 0.000 1.00 0.00
ATOM 13 C1 PEt 3 3.910 2.000 3.000 1.00 0.00
ATOM 14 H11 PEt 3 0.000 0.000 0.000 1.00 0.00
ATOM 15 H12 PEt 3 0.000 0.000 0.000 1.00 0.00
ATOM 16 C2 PEt 3 5.360 8.000 4.000 1.00 0.00
ATOM 17 H21 PEt 3 0.000 0.000 0.000 1.00 0.00
ATOM 18 H22 PEt 3 0.000 0.000 0.000 1.00 0.00
TER
ENDMDL
*[Question #3 from If... section ]*
I guess that I have to change hdb and tdb files.
Would you please give some guide on that...?
Thank you for your care!
Sincerely yours,
C Kim
On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Chansoo Kim wrote:
Dear Dr. Benkova and others:
I am C. Kim and trying to simulation polymer system.
Since I guessed that polyethylene (PE) is a simple system, it could be
not that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing
list to tackle my problems.
Sorry to say, I could not solve problems, so I am asking your help!
Actually I have used your files written in followings,
http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html
[Q1]
After getting the result from the pdb2gmx, I could not see any H-atoms
in my system.
All the H-atoms have 0, 0, 0 positions!
Therefore, my question is
how I should define hdb?
The .hdb file format is explained in the manual.
[Q2]
When I use -C2, and +C1 in hdb file, I always meet error.
What is the error?
-Justin
Is there any other things to add to the ffopls*.* files...?
Thank you for your care!
Sincerely
C. Kim
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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