[gmx-users] Polyethylene (PE) simulations in Gromacs - please!
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 3 15:47:19 CET 2009
I took a few minutes to look into this. Since I have seen these same,
incomplete posts that give no solution, let me propose one. I was able to
produce an OPLS-AA PE topology with pdb2gmx using the following additions to the
corresponding .rtp and .hdb files:
ffoplsaa.rtp:
; Polyethylene - this is an internal residue
[ 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 -C2
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 +C1
; Terminal PE residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
[ EthB ]
[ atoms ]
C1 opls_135 -0.180 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
H13 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 H13
C1 C2
C2 H21
C2 H22
C2 +C1
; Terminal PE residue ("end" of chain)
; designation arbitrary, C2 is -CH3
[ EthE ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_135 -0.180 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
H23 opls_140 0.060 2
[ bonds ]
C1 -C2
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 H23
ffoplsaa.hdb:
Eth 2
2 6 H1 C1 C2 -C2
2 6 H2 C2 C1 +C1
EthB 2
3 4 H1 C1 C2 +C1
2 6 H2 C2 C1 +C1
EthE 2
2 6 H1 C1 C2 -C2
3 4 H2 C2 C1 -C2
I successfully created a topology from pdb2gmx using this .pdb file:
ATOM 1 C1 EthB 1 1.000 1.540 0.000
ATOM 2 C2 EthB 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 EthE 3 3.912 5.623 0.000
ATOM 6 C2 EthE 3 5.368 6.124 0.000
END
I think the main reason the -n.tdb and -c.tdb modifications do not work is the
following message from pdb2gmx: "No N- or C-terminus found: this chain appears
to contain no protein."
I do not vouch for the validity of these parameters, as I have no need to test
them. This information is only meant to be instructive regarding using pdb2gmx
to generate a topology; it is an exercise for the user to determine whether or
not such parameters are valid.
-Justin
Zuzana Benkova wrote:
> 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-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Chansoo Kim
> *Sent:* Tuesday, March 03, 2009 2:50 PM
> *To:* jalemkul at 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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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 gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> 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 gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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 gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list