[gmx-users] CHARMM36: No default U-B types
Justin Lemkul
jalemkul at vt.edu
Thu Sep 4 20:56:55 CEST 2014
On 9/4/14, 2:51 PM, Victor Sojo wrote:
> Hi all!
>
> We're trying to use a DPhPG (i.e. archaeal/non-standard) lipid bilayer on
> CHARMM36.
>
> I put the lipid into ParamChem, (having previously added hydrogens and
> converted to mol2 format).
> I then put the parameters into the merged.rtp file in the
> charmm36-mar2014.ff folder.
> Then pdb2gmx to generate a topology file for the lipid. So far so good.
> When trying to do an energy minimisation of just one such lipid, I get the
> errors of the following type (4 for U-B type and 17 for dihedrals, please
> see all the errors at the end).
>
> ERROR 1 [file dphpg.itp, line 756]:
> No default U-B types
>
> All the errors seem to involve the two oxygen atoms in the ether-linkages
> of the archaeal lipid.
> The curious thing is that line 756 of the lipid topology, for example, has
> three atoms that actually are specified in the [ angles ] field. So, I'm
> wondering where I went wrong. For all lipids previously included by default
> in merged.rtp, the only three fields I can see are [ atoms ] [ bonds ]
> and [ impropers ]. I put [ angles ] and [ dihedrals ] in myself from
> the results of ParamChem, but I don't know if there is something wrong.
>
> This is the end of the text I put into merged.rtp:
> HC87 C55
> HC88 C55
> HC89 C56
> HC90 C56
> HC91 C56
> [ angles ]
> CG321 CG311 OG301 115.00 109.70 ! dphpg1. , from CG321 CG311 OG302,
> penalty= 0.5
> CG311 CG321 OG301 75.70 110.10 ! dphpg1. , from CG311 CG321 OG302,
> penalty= 0.5
> CG311 OG301 CG321 95.00 109.70 ! dphpg1. , from CG321 OG301 CG321,
> penalty= 0.6
> [ dihedrals ]
> CG321 CG311 CG321 OG301 0.2000 3 180.00 ! dphpg1. , from CG321
> CG311 CG321 OG302, penalty= 0.5
> OG301 CG311 CG321 OG301 0.2000 3 0.00 ! dphpg1. , from OG302
> CG311 CG321 OG302, penalty= 1
> OG301 CG311 CG321 OG303 0.2000 3 0.00 ! dphpg1. , from OG302
> CG311 CG321 OG303, penalty= 0.5
> OG301 CG311 CG321 HGA2 0.1950 3 0.00 ! dphpg1. , from OG302
> CG311 CG321 HGA2, penalty= 0.5
> HGA1 CG311 CG321 OG301 0.1950 3 0.00 ! dphpg1. , from HGA1
> CG311 CG321 OG302, penalty= 0.5
> CG321 CG311 OG301 CG321 0.4000 1 0.00 ! dphpg1. , from CG331
> CG311 OG301 CG331, penalty= 1.8
> CG321 CG311 OG301 CG321 0.4900 3 0.00 ! dphpg1. , from CG331
> CG311 OG301 CG331, penalty= 1.8
> HGA1 CG311 OG301 CG321 0.2840 3 0.00 ! dphpg1. , from HGA1
> CG311 OG301 CG331, penalty= 0.9
> CG311 CG321 CG321 OG301 0.1600 1 180.00 ! dphpg1. , from CG321
> CG321 CG321 OG301, penalty= 0.6
> CG311 CG321 CG321 OG301 0.3900 2 0.00 ! dphpg1. , from CG321
> CG321 CG321 OG301, penalty= 0.6
> CG311 CG321 OG301 CG321 0.5700 1 0.00 ! dphpg1. , from CG321
> CG321 OG301 CG321, penalty= 0.6
> CG311 CG321 OG301 CG321 0.2900 2 0.00 ! dphpg1. , from CG321
> CG321 OG301 CG321, penalty= 0.6
> CG311 CG321 OG301 CG321 0.4300 3 0.00 ! dphpg1. , from CG321
> CG321 OG301 CG321, penalty= 0.6
> CG321 CG321 OG301 CG311 0.5700 1 0.00 ! dphpg1. , from CG321
> CG321 OG301 CG321, penalty= 0.6
> CG321 CG321 OG301 CG311 0.2900 2 0.00 ! dphpg1. , from CG321
> CG321 OG301 CG321, penalty= 0.6
> CG321 CG321 OG301 CG311 0.4300 3 0.00 ! dphpg1. , from CG321
> CG321 OG301 CG321, penalty= 0.6
> HGA2 CG321 OG301 CG311 0.2840 3 0.00 ! dphpg1. , from HGA2
> CG321 OG301 CG321, penalty= 0.6
>
All of these lines are going to be misinterpreted because of the text that is in
CHARMM comment format (after the !) instead of Gromacs format (using ; for
comments), and it's a wonder that pdb2gmx even works.
You should introduce any new bonded parameters in ffbonded.itp or use our Python
converter to get a suitable Gromacs topology.
-Justin
>
> Here's a sample of the atoms definition:
> 13 CG321 1 DPGG C12 13 -0.077 12.011 ;
> qtot -1.629
> 14 CG311 1 DPGG C13 14 0.087 12.011 ;
> qtot -1.542
> 15 OG301 1 DPGG O14 15 -0.35 15.9994 ;
> qtot -1.892
> 16 CG321 1 DPGG C15 16 -0.005 12.011 ;
> qtot -1.897
> 17 CG321 1 DPGG C16 17 -0.184 12.011 ;
> qtot -2.081
> ...where you can see the three atoms involved in Error 1 (line 756) are
> actually defined above
>
> Below is line 756, just in case:
> [ angles ]
> ; ai aj ak funct c0 c1 c2
> c3
> .....
> 13 14 15 5
> ....
>
> And these are all the errors I get:
>
> ERROR 1 [file dphpg.itp, line 756]:
> No default U-B types
>
> ERROR 2 [file dphpg.itp, line 759]:
> No default U-B types
>
> ERROR 3 [file dphpg.itp, line 762]:
> No default U-B types
>
> ERROR 4 [file dphpg.itp, line 883]:
> No default U-B types
>
> ERROR 5 [file dphpg.itp, line 1049]:
> No default Proper Dih. types
>
> ERROR 6 [file dphpg.itp, line 1052]:
> No default Proper Dih. types
>
> ERROR 7 [file dphpg.itp, line 1055]:
> No default Proper Dih. types
>
> ERROR 8 [file dphpg.itp, line 1058]:
> No default Proper Dih. types
>
> ERROR 9 [file dphpg.itp, line 1059]:
> No default Proper Dih. types
>
> ERROR 10 [file dphpg.itp, line 1060]:
> No default Proper Dih. types
>
> ERROR 11 [file dphpg.itp, line 1061]:
> No default Proper Dih. types
>
> ERROR 12 [file dphpg.itp, line 1064]:
> No default Proper Dih. types
>
> ERROR 13 [file dphpg.itp, line 1065]:
> No default Proper Dih. types
>
> ERROR 14 [file dphpg.itp, line 1066]:
> No default Proper Dih. types
>
> ERROR 15 [file dphpg.itp, line 1067]:
> No default Proper Dih. types
>
> ERROR 16 [file dphpg.itp, line 1070]:
> No default Proper Dih. types
>
> ERROR 17 [file dphpg.itp, line 1071]:
> No default Proper Dih. types
>
> ERROR 18 [file dphpg.itp, line 1072]:
> No default Proper Dih. types
>
> ERROR 19 [file dphpg.itp, line 1073]:
> No default Proper Dih. types
>
> ERROR 20 [file dphpg.itp, line 1244]:
> No default Proper Dih. types
>
> ERROR 21 [file dphpg.itp, line 1250]:
> No default Proper Dih. types
>
>
> Any help would be greatly appreciated!
>
>
> Vic.
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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