[gmx-users] Re: berger-oplsaa combination for DPC micelle
Low Soo Mei
lowsm at bii.a-star.edu.sg
Fri Jun 6 05:15:58 CEST 2008
Thanks again. I will try to figure out something without actually
adding in the missing bondtypes / angletypes / dihedraltypes....
Interestingly (or perhaps not so surprisingly) PRODRG does not support
the creation of a dpc.itp in the modified berger-oplsaa forcefield.
Thanks,
Soo Mei
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 05 Jun 2008 13:25:44 -0400
> From: chris.neale at utoronto.ca
> Subject: [gmx-users] berger-oplsaa combination for DPC micelle
> To: gmx-users at gromacs.org
> Message-ID: <20080605132544.icrhw0583cw0o400 at webmail.utoronto.ca>
> 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.
>
>
>> 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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