<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Thanks again. I will try to figure out something without actually
adding in the missing bondtypes / angletypes / dihedraltypes....<br>
<br>
Interestingly (or perhaps not so surprisingly) PRODRG does not support
the creation of a dpc.itp in the modified berger-oplsaa forcefield.<br>
<br>
Thanks,<br>
Soo Mei<br>
<blockquote cite="mid:20080605225052.B88D42435F@xray.bmc.uu.se"
type="cite">
<pre wrap="">
----------------------------------------------------------------------
Message: 1
Date: Thu, 05 Jun 2008 13:25:44 -0400
From: <a class="moz-txt-link-abbreviated" href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>
Subject: [gmx-users] berger-oplsaa combination for DPC micelle
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:20080605132544.icrhw0583cw0o400@webmail.utoronto.ca"><20080605132544.icrhw0583cw0o400@webmail.utoronto.ca></a>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Hi Soo Mei,
I think that the error messages that you post are pretty descriptive.
You can definitely use them to figure out what you are missing. I am
not currently distributing my dpc.itp file beyond the snippit and
instructions that I posted earlier.
Chris.
</pre>
<blockquote type="cite">
<pre wrap="">I'm sorry, the line references are for the dpc_double_pairlist.itp file
I have posted. I should have made that clearer.
Lines 68-86 are the 4th line of [ bonds ] till the last line of [ bonds]
. Lines 138 and 147 are the 8th line and 17th line of [ angles ].
Lines 161-167 are the first 7 lines of [ dihedrals ].
For completeness I also attach here the ffoplsaanb.itp and
ffoplsaabon.itp modified according to the half-epsilon double-pairlist
method. These forcefield .itp files are in my working directory and are
read in in full during my failed grompp for minimization, when I checked
the output .top of this failed grompp. I had called them using
#include "ffoplsaa.itp" , the default ffoplsaa.itp not in my working
directory. grompp command was grompp -v -f min.mdp -c
enlarged_merged_solvated_internalwatersremoved.pdb -p berger_opls.top
-po test_min1out.mdp -pp test_min1out.top -o min1.tpr
Thank you in advance for your advice. I am completely stuck at this step.
Cheers,
Soo Mei
-------- Original Message --------
Subject: Re: berger-oplsaa combination for DPC micelle
Date: Thu, 05 Jun 2008 02:42:58 +0800
From: Low Soo Mei <a class="moz-txt-link-rfc2396E" href="mailto:lowsm@bii.a-star.edu.sg"><lowsm@bii.a-star.edu.sg></a>
Organization: BII
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
References: <a class="moz-txt-link-rfc2396E" href="mailto:20080604160204.C2FA92435F@xray.bmc.uu.se"><20080604160204.C2FA92435F@xray.bmc.uu.se></a>
Hi,
Thank you Chris for the helpful answer! I have modified the atomtype
names to follow dmpc.itp, which is more familiar to me, but those names
are also the same as popc.itp. There is probably something wrong with
the way I did it because although the "atomtype not found" errors have
stopped, I am getting "no default bond types (lines 68-86) / angle types
(lines 138, 147) / proper dihedral types (lines 161-167)". My modified
dpc_double_pairlist.itp file is attached below.
</pre>
<blockquote type="cite">
<pre wrap="">Message: 7
Date: Wed, 04 Jun 2008 12:01:33 -0400
From: <a class="moz-txt-link-abbreviated" href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>
Subject: [gmx-users] berger-oplsaa combination for DPC micelle
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:20080604120133.htonx5kcw8gg8c48@webmail.utoronto.ca"><20080604120133.htonx5kcw8gg8c48@webmail.utoronto.ca></a>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
In general, you should always post your relevant files with your
question. It makes it easier for us to answer you. That said, I happen
to have already used DPC and here is what I have done. I made a new
dpc_rename.itp and it is quite different, but should simulate the
exact same. Here is the beginning of the atoms section
;Chris Neale modified atomtype names here to follow popc.itp
; Atoms double checked vs. popc.itp by CN Oct5 2006
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 LC3 1 DPC C1 1 0.4 ;
qtot: 0.248
2 LC3 1 DPC C2 1 0.4 ;
qtot: 0.496
3 LC3 1 DPC C3 1 0.4 ;
qtot: 0.744
4 LNL 1 DPC N4 1 -0.5 ;
qtot: 0.752
5 LH2 1 DPC C5 1 0.3 ; qtot: 1
and then you need to make modifications to the other sections so that
the parameters are found appropriately.
Chris.
-- original message --
Hi Gromacs users,
I am trying to simulate a protein with a micelle, and have used dpc.itp
from Dr. Tieleman's site. I have also introduced parts of lipid.itp
into ffoplsaanb.itp and ffoplsaabon.itp in accordance with Chris Neale's
half-epsilon double-pairlist method. But when I issue a grompp command
for minimization, grompp gives a fatal error that the "Bonded/nonbonded
atom type 'CH3' not found!". This atom type CH3 is present in dpc.itp.
I am now wondering if I can match this to some existing atom in the
oplsaa and how I might go about choosing which atom.
I would be grateful for your advice, and am happy to attach files if needed.
Cheers,
Soo Mei
</pre>
</blockquote>
<pre wrap="">dpc_double_pairlist.itp:
; topology for a dodecylphosphocholine lipid from Tieleman's site.
; modified to follow the other pc.itp's on Tieleman's site, as suggested
by Chris Neale on gmx-users list on 4th June 2008, when I had "atomtype
not found" problems
[ bondtypes ]
; i j func b0 kb
LC3 LNL 1 0.14700 376560. ; formerly CH3 and NL.
; CH1 OS 1 0.14300 251040. ; no CH1 in DPC.
; OS C 1 0.13600 251040. ; no C in DPC. C is the
ester-linkage carbon that joins the glycerol backbone to the long lipid
chains in the pc.itp's.
[ angletypes ]
; i j k func th0 cth
LC3 LNL LC3 1 109.500 460.00 ; formerly CH3 NL CH3
LC3 LNL LH2 1 109.500 460.00 ; formerly CH3 NL CH2
; CH2 CH1 OS 1 109.500 460.00 ; no CH1 in DPC.
LNL LH2 LC2 1 109.500 460.00 ; formerly NL CH2 CH2
LP LOS LC2 1 120.000 397.00 ; formerly P OS CH2. Can't
decide if it's 8 7 6 or 8 11 12. Will put for both. This is 8 7 6
LP LOS LP2 1 120.000 397.00 ; and this is 8 11 12.
LOS LP LOM 1 109.600 397.00 ; formerly OS P OM
LOS LP LOS 1 103.000 397.00 ; formerly OS P OS
LOM LP LOM 1 120.000 585.00 ; formerly OM P OM
; OS CH2 CH1 1 111.000 460.00 ; no CH1 in DPC.
; CH2 CH2 CH1 1 111.000 460.00 ; no CH1 in DPC.
LP2 LP2 LP2 1 111.000 460.00
LP2 LP2 LP3 1 111.000 460.00
; CH2 CH1 CH2 1 109.500 460.00 ; no CH1 in DPC.
; CH1 OS C 1 120.000 418.00 ; no CH1 or C in DPC.
; CH2 OS C 1 120.000 418.00 ; no C in DPC.
; CH3 OS C 1 120.000 418.00 ; no C in DPC.
; OS C O 1 124.000 502.00 ; no C in DPC.
; OS C CH2 1 115.000 502.00 ; no C in DPC.
; O C CH2 1 121.000 502.00 ; no C in DPC.
; C CH2 CH2 1 120.000 585.00 ; no C in DPC.
[ moleculetype ]
; Name nrexcl
DPC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 LC3 1 DPC C1 1 0.4 ;
qtot: 0.248, type formerly CH3
2 LC3 1 DPC C2 1 0.4 ;
qtot: 0.496, type formerly CH3
3 LC3 1 DPC C3 1 0.4 ;
qtot: 0.744, type formerly CH3
4 LNL 1 DPC N4 1 -0.5 ;
qtot: 0.752, type formerly NL
5 LH2 1 DPC C5 1 0.3 ;
qtot: 1, type formerly CH2
6 LC2 1 DPC C6 1 0.4 ;
qtot: 1, type formerly CH2
7 LOS 1 DPC O7 1 -0.8 ;
qtot: 0.64, type formerly OS
8 LP 1 DPC P8 1 1.7 ;
qtot: 1.64, type formerly P
9 LOM 1 DPC O9 1 -0.8 ;
qtot: 1, type formerly OM
10 LOM 1 DPC O10 1 -0.8 ;
qtot: 0.36, type formerly OM
11 LOS 1 DPC O11 1 -0.7 ;
qtot: 0, type formerly OS
12 LP2 1 DPC C12 5 0 ;
qtot: 0, type formerly CH2
13 LP2 1 DPC C13 6 0 ;
qtot: 0, type formerly CH2
14 LP2 1 DPC C14 7 0 ;
qtot: 0, type formerly CH2
15 LP2 1 DPC C15 8 0 ;
qtot: 0, type formerly CH2
16 LP2 1 DPC C16 9 0 ;
qtot: 0, type formerly CH2
17 LP2 1 DPC C17 10 0 ;
qtot: 0, type formerly CH2
18 LP2 1 DPC C18 11 0 ;
qtot: 0, type formerly CH2
19 LP2 1 DPC C19 12 0 ;
qtot: 0, type formerly CH2
20 LP2 1 DPC C20 13 0 ;
qtot: 0, type formerly CH2
21 LP2 1 DPC C21 14 0 ;
qtot: 0, type formerly CH2
22 LP2 1 DPC C22 15 0 ;
qtot: 0, type formerly CH2
23 LP3 1 DPC C23 16 0 ;
qtot: 0, type formerly CH3
[ bonds ]
; ai aj funct
1 4 1
2 4 1
3 4 1
4 5 1
5 6 1
6 7 1
7 8 1
8 9 1
8 10 1
8 11 1
11 12 1
12 13 1
13 14 1
14 15 1
15 16 1
16 17 1
17 18 1
18 19 1
19 20 1
20 21 1
21 22 1
22 23 1
[ pairs ]
; ai aj funct
; Here is the first copy.
1 6 1
2 6 1
3 6 1
4 7 1
5 8 1
6 9 1
6 10 1
6 11 1
7 12 1
8 13 1
9 12 1
10 12 1
11 14 1
; 12 15 1
; 13 16 1
; 14 17 1
; 15 18 1
; 16 19 1
; 17 20 1
; 18 21 1
; 19 22 1
; 20 23 1
; Here is the second copy. Only use this with the halved LJ-14 epsilon
values.
1 6 1
2 6 1
3 6 1
4 7 1
5 8 1
6 9 1
6 10 1
6 11 1
7 12 1
8 13 1
9 12 1
10 12 1
11 14 1
[ angles ]
; ai aj ak funct
1 4 2 1
1 4 3 1
1 4 5 1
2 4 3 1
2 4 5 1
3 4 5 1
4 5 6 1
5 6 7 1
6 7 8 1
7 8 9 1
7 8 10 1
7 8 11 1
9 8 10 1
9 8 11 1
10 8 11 1
8 11 12 1
11 12 13 1
12 13 14 1
13 14 15 1
14 15 16 1
15 16 17 1
16 17 18 1
17 18 19 1
18 19 20 1
19 20 21 1
20 21 22 1
21 22 23 1
[ dihedrals ]
; ai aj ak al funct
1 4 5 6 1
4 5 6 7 1
5 6 7 8 1
6 7 8 9 1
7 8 11 12 1
8 11 12 13 1
11 12 13 14 1
12 13 14 15 3
13 14 15 16 3
14 15 16 17 3
15 16 17 18 3
16 17 18 19 3
17 18 19 20 3
18 19 20 21 3
19 20 21 22 3
20 21 22 23 3
ffoplsaanb.itp:
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
; added by soo mei and devan on 4th June 2008
LO LO 15.9994 0.000 A 0.296 0.878693
LOM LOM 15.9994 0.000 A 0.296 0.878693
LNL LNL 14.0067 0.000 A 0.324997 0.711373
LC LC 12.0110 0.000 A 0.374986 0.439521
LH1 LH1 13.0190 0.000 A 0.380015 0.334617
LH2 LH2 14.0270 0.000 A 0.390504 0.493637
LP LP 30.9738 0.000 A 0.374004 0.836713
LOS LOS 15.9994 0.000 A 0.299989 0.879137
LP2 LP2 14.0270 0.000 A 0.395994 0.38084
LP3 LP3 15.0350 0.000 A 0.396006 0.568952
LC3 LC3 15.0350 0.000 A 0.396012 0.606495
LC2 LC2 14.0270 0.000 A 0.379979 0.493945
...
[ pairtypes ]
; added by soo mei and devan on 4th June 2008
; i j func sigma halved_epsilon
LO LO 1 0.296038 0.0548205
LO LOM 1 0.296038 0.0548205
LO opls_116 1 0.306317 0.0473315
LO LNL 1 0.310178 0.0493787
LO LC 1 0.333186 0.0387945
LO LH1 1 0.335422 0.0338365
LO LH2 1 0.340009 0.0411152
LO LP 1 0.332746 0.0535345
LO LOS 1 0.297989 0.0548975
LO LP2 1 0.342367 0.0361464
LO LP3 1 0.342395 0.0441426
LO LC3 1 0.342385 0.0455935
LO LC2 1 0.335388 0.0411466
LOM LOM 1 0.296038 0.0548205
LOM opls_116 1 0.306317 0.0473315
LOM LNL 1 0.310178 0.0493787
LOM LC 1 0.333186 0.0387945
LOM LH1 1 0.335422 0.0338365
LOM LH2 1 0.340009 0.0411152
LOM LP 1 0.332746 0.0535345
LOM LOS 1 0.297989 0.0548975
LOM LP2 1 0.342367 0.0361464
LOM LP3 1 0.342395 0.0441426
LOM LC3 1 0.342385 0.0455935
LOM LC2 1 0.335388 0.0411466
opls_116 LNL 1 0.320955 0.0426192
opls_116 LC 1 0.344783 0.0334699
opls_116 LH1 1 0.347079 0.0292101
opls_116 LH2 1 0.351809 0.0355021
opls_116 LP 1 0.344302 0.046215
opls_116 LOS 1 0.308362 0.0473692
opls_116 LP2 1 0.354267 0.0311978
opls_116 LP3 1 0.354273 0.0381177
opls_116 LC3 1 0.354276 0.0393613
opls_116 LC2 1 0.347048 0.0355144
LNL LNL 1 0.325001 0.0444655
LNL LC 1 0.349124 0.0349218
LNL LH1 1 0.351449 0.0304739
LNL LH2 1 0.356251 0.0370305
LNL LP 1 0.348642 0.0482144
LNL LOS 1 0.312236 0.0494409
LNL LP2 1 0.358753 0.0325351
LNL LP3 1 0.358767 0.0397492
LNL LC3 1 0.358753 0.0410602
LNL LC2 1 0.35139 0.0370716
LC LC 1 0.375036 0.0274302
LC LH1 1 0.37751 0.0239465
LC LH2 1 0.382703 0.0290762
LC LP 1 0.374519 0.0378681
LC LOS 1 0.335418 0.038816
LC LP2 1 0.385354 0.0255642
LC LP3 1 0.385387 0.0312205
LC LC3 1 0.385369 0.032252
LC LC2 1 0.37751 0.0290941
LH1 LH1 1 0.380041 0.0208895
LH1 LH2 1 0.385255 0.0253742
LH1 LP 1 0.377008 0.0330493
LH1 LOS 1 0.337649 0.0338775
LH1 LP2 1 0.387935 0.022305
LH1 LP3 1 0.387966 0.0272392
LH1 LC3 1 0.387944 0.0281396
LH1 LC2 1 0.380031 0.0253867
LH2 LH2 1 0.390543 0.0308181
LH2 LP 1 0.382176 0.0401572
LH2 LOS 1 0.342275 0.0411569
LH2 LP2 1 0.393236 0.0270987
LH2 LP3 1 0.393276 0.0330925
LH2 LC3 1 0.393237 0.0342109
LH2 LC2 1 0.385233 0.0308442
LP LP 1 0.373989 0.0523075
LP LOS 1 0.334959 0.053589
LP LP2 1 0.384828 0.0352884
LP LP3 1 0.384887 0.0430654
LP LC3 1 0.384866 0.0445026
LP LC2 1 0.376986 0.0401721
LOS LOS 1 0.299979 0.054944
LOS LP2 1 0.344642 0.0361853
LOS LP3 1 0.344676 0.0441854
LOS LC3 1 0.344657 0.0456467
LOS LC2 1 0.337624 0.0411842
LP2 LP2 1 0.395957 0.0238272
LP2 LP3 1 0.395999 0.0290924
LP2 LC3 1 0.395992 0.0300486
LP2 LC2 1 0.387888 0.0271217
LP3 LP3 1 0.39601 0.0355533
LP3 LC3 1 0.395997 0.0367273
LP3 LC2 1 0.387918 0.0331251
LC3 LC3 1 0.395987 0.0379324
LC3 LC2 1 0.387907 0.0342131
LC2 LC2 1 0.379982 0.0308754
ffoplsaabon.itp:
[ dihedraltypes ]
; i j k l func coefficients
; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form
; according to the formula in the Gromacs manual.
;added by soo mei and devan on 4th June 2008
LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
LH2 LH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
</body>
</html>