[gmx-users] CHARMM36: No default U-B types

[Victor Sojo]

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


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.