[gmx-users] berger-oplsaa combination for DPC micelle
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Thu Jun 5 19:25:44 CEST 2008
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.
> 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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