[gmx-users] Re: berger-oplsaa combination for DPC micelle

Low Soo Mei lowsm at bii.a-star.edu.sg
Thu Jun 5 19:11:51 CEST 2008


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 <lowsm at bii.a-star.edu.sg>
Organization: 	BII
To: 	gmx-users at gromacs.org
References: 	<20080604160204.C2FA92435F at xray.bmc.uu.se>



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.

> Message: 7
> Date: Wed, 04 Jun 2008 12:01:33 -0400
> From: chris.neale at utoronto.ca
> Subject: [gmx-users] berger-oplsaa combination for DPC micelle
> To: gmx-users at gromacs.org
> Message-ID: <20080604120133.htonx5kcw8gg8c48 at webmail.utoronto.ca>
> 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
>
>   

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





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