Chansoo Kim wrote:
Dear Justin:
Please call me, 'chance'.
I have been doing neutron scattering and MD on water.
Thank you again for this conversation with you, Justin.
Right now, I am trying to do polymer simulation to mimic an interaction
with a plasma.
To do so, I am targeting PE system.
Related to the my question related to the [Error] and [Question #1],
[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C2 not found in residue PEth1 while adding hydrogens"
You can't specify a previous residue (designated by -) from the first residue in
a chain. Hence why I suggested what I did before about special terminal
residues. See the post I just sent about functioning .rtp and .hdb entries,
they worked for me.
-Justin
[Question #1]
Therefore, what I should define more...?
I cannot avoid to ask you this question again!
As I emailed you, since I corrected error related to "blank" in the
input files (pdb and etc.), it has never given me "segmentation fault."
The only error that the gromacs gives me is the above one.
Even though I am following your suggestion in the previous email, I want
to clarify the above problem.
Do you have any idea on this...?
Thank you again!!
Sincerely yours,
Chance
(PS) The "chemical reaction", which I wrote in the second email, is my
mistake. I did not mean "chemical reaction"... And I appreciate that you
pointed it out.
On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Chansoo Kim wrote:
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...
No chemical reactions occur :) See comments embedded below
[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
Note that the message you referenced in your first post (which
provided you with this .rtp entry) resulted in a segmentation fault,
therefore indicating that it probably won't work.
(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?
+ means next residue, - means previous.
[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).
Right, because H positioning in a polymer chain may depend on
previous (-) or subsequent (+) residues, so the code doesn't know
where to put them.
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...?
Knowing that many people have tried to define PE with .tdb entries
(and I think success is limited), I would suggest the following.
Define distinct .rtp entries for the caps of your chain. Don't
bother with -n.tdb and -c.tdb; I don't know how well the Gromacs
code handles non-protein termini (maybe it works, but it seems to
give fits for polymers). The .rtp entry for PE you've shown above
seems reasonable enough for a PE monomer within the chain, but may
require some tweaking (since I've never tried, I don't know).
-Justin
Thank you for your care!
Sincerely yours,
C Kim
On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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/[email protected]/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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
