Justin:
Thank you very much! It worked and everything seems reasonable now.
Regards,
Tengfei
----- Original Message -----
From: "Justin A. Lemkul" <jalem...@vt.edu>
To: "Gromacs Users' List" <gmx-users@gromacs.org>
Sent: Wednesday, November 18, 2009 2:47 PM
Subject: Re: [gmx-users] how to construct fatty acid
When I run grompp using all your files, I get a series of errors:
ERROR 1 [file topol.top, line 60]:
No default Bond types
ERROR 2 [file topol.top, line 144]:
No default Angle types
ERROR 3 [file topol.top, line 190]:
No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 191]:
No default Ryckaert-Bell. types
How did you deal with these? The first refers to the OT-HO bond, for
which there is no known bond type, and the rest are a result of the same
problematic atom types.
I think you have the carboxylate oxygen types wrong. The carbonyl O
should be opls_269, and the acid O (in the -OH functional group) should be
opls_268. These atom types are taken from the ASPH .rtp entry. If you
switch them, the errors go away and the structure produced seems
reasonable.
-Justin
Tengfei Luo wrote:
Here it is:
title = acid
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIBLE ; use flexible water model
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
Thank you again!
Tengfei
----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu>
To: "Gromacs Users' List" <gmx-users@gromacs.org>
Sent: Wednesday, November 18, 2009 2:34 PM
Subject: Re: [gmx-users] how to construct fatty acid
Tengfei Luo wrote:
Justin:
Thank you for your help!
Yes, the OH bond length changed before and after minimization. and yes,
the H get close to the carbonyl O in the COOH group. I did the
minimization with solvent.
I appreciate any further suggestion!
Can you post your .mdp file? I have never seen any instability in
OPLS -COOH groups like you've described.
-Justin
Tengfei
----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Wednesday, November 18, 2009 2:21 PM
Subject: Re: [gmx-users] how to construct fatty acid
Tengfei Luo wrote:
Dear All:
I'm new to Gromacs. I want to simulate water disolve in fatty acid
(C-C-COOH) using a all atom model. I started up with constructing the
pdb file of decanoic acid. Following the post by Justin
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I
added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also
added the following [COOH] section into this file
; cooh
[ COOH ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_267 0.52 2
O opls_268 -0.530 2
OT opls_269 -0.44 2
HO opls_270 0.45 2
[ bonds ]
C1 -C2
C1 H11
C1 H12
C1 C2
C2 O
C2 OT
OT HO
[ impropers ]
C1 OT C2 O improper_O_C_X_Y
The following lines are also added to the .hdb file inaddition to
those suggested in the aformentioned link
COOH 2
2 6 H1 C1 C2 -C2
1 2 HO OT C2 C1
My pdb file is
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 COOH 3 3.912 5.623 0.000
ATOM 6 C2 COOH 3 5.368 6.124 0.000
ATOM 7 O COOH 3 6.800 6.124 0.000
ATOM 8 OT COOH 3 5.300 7.600 0.000
END
I successfully constructed the .top file using pdb2gmx. However, when
doing minimization, I found that the H attached to the O get too
close to this O atom. I notice that there is no bond between these
two atoms in the top file (a part of the top file is attached as
follow):
Does the bond length change somehow? Or does the H get close to the
carbonyl oxygen in the -COOH group? Are you doing the minimization in
vacuo? If so, the strong (condensed-phase) charges that you have
assigned may be inappropriate in the absence of solvent, which will
screen electrostatic effects.
<snip>
The topology looks reasonable.
Do you see what is wrong with my approach? I also know there is -ter
which can replace the end with COOH, but how can I construct the
termini to be replace at the first place?
The -ter option does not function for non-protein compounds, as stated
in the thread you cite.
-Justin
I tried to make myself as clear as possible and make the email short.
I shall appreciate any help or suggestion.
Sincerely,
Tengfei
--
========================================
Justin A. Lemkul
Ph.D. Candidate
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
========================================
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========================================
Justin A. Lemkul
Ph.D. Candidate
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
========================================
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Please search the archive at http://www.gromacs.org/search before
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
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
========================================
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