[gmx-users] .itp file of choline molecule

[soumadwip ghosh]

Dear users,
                    I am studying the dynamics of a double stranded DNA in
presence of choline counterion. I am using GROMACS 4.5.6 and CHARMM27 force
field for MD simulations. Initially, I made the united atom PDB for Choline
using ATB topology biliding software. Since the PDB was specifically meant
for GROMOS forcefield, I copied the PDB in my working directory and added [
CHO ] in the aminoacid.rtp according to the ones specified in atomtypes.atp
of CHARMM27 force field directory. My PDB file looks like -

DER    UNCLASSIFIED                            05-Dec-14
TITLE     UNITED ATOM STRUCTURE FOR MOLECULE CHO
AUTHOR    GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2014-09-22
AUTHOR   2  http://compbio.biosci.uq.edu.au/atb
HETATM    1   O6 CHO     0      -2.169   0.657   0.155  1.00  0.00
  O
HETATM    2  H14 CHO     0      -3.029   0.566   0.595  1.00  0.00
  H
HETATM    3   C4 CHO     0      -1.635  -0.644  -0.037  1.00  0.00
  C
HETATM    4   C5 CHO     0      -0.300  -0.549  -0.758  1.00  0.00
  C
HETATM    5   N1 CHO     0       0.876   0.042   0.022  1.00  0.00
  N1+
HETATM    6   C8 CHO     0       2.088  -0.022  -0.875  1.00  0.00
  C
HETATM    7   C7 CHO     0       0.630   1.486   0.391  1.00  0.00
  C
HETATM    8   C6 CH0     0       1.156  -0.753   1.269  1.00  0.00
  C
CONECT    1    2    3
CONECT    2    1
CONECT    3    1    4
CONECT    4    3    5
CONECT    5    4    6    7    8
CONECT    6    5
CONECT    7    5
CONECT    8    5
END

The [ choline ] part in aminoacid.rtp looks like-

[ CHO ]
[ atoms ]
   O6   OH1  -0.66    1
   H14  H     0.31    2
   C4  CTL2   0.30    3
   C5  CTL2   0.30    4
   N1  NH3   -0.30    5
   C8  CTL5   0.35    6
   C7  CTL5   0.35    7
   C6  CTL5   0.35    8
[ bonds ]
O6  H14
O6  C4
H14 O6
C4  O6
C4  C5
C5  N1
C8  N1
C7  N1
C6  N1

Then I did pdb2gmx -f cholineua.pdb to make the topology of choline. It
proceeded smoothly and I made the choline.itp file from the .top file
created and it looks like-


  File 'topol.top' was generated
;       By user: onbekend (0)
;       On host: onbekend
;       At date: Fri Dec  5 04:28:53 2014
;
;       This is a standalone topology file
;
;       It was generated using program:
;       pdb2gmx - VERSION 4.5.6
;
;       Command line was:
;       pdb2gmx -f cholineua.pdb
;
;       Force field was read from current directory or a relative path -
path added.
;

; Include forcefield parameters

[ moleculetype ]
; Name            nrexcl
CHO               3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
; residue   0 CHO rtp CHO  q +1.0
     1        OH1      0    CHO     O6      1      -0.66     15.999   ;
qtot -0.66
     2          H      0    CHO    H14      2       0.31      1.008   ;
qtot -0.35
     3       CTL2      0    CHO     C4      3        0.3     12.011   ;
qtot -0.05
     4       CTL2      0    CHO     C5      4        0.3     12.011   ;
qtot 0.25
     5        NH3      0    CHO     N1      5       -0.3     14.007   ;
qtot -0.05
     6       CTL5      0    CHO     C8      6       0.35     12.011   ;
qtot 0.3
     7       CTL5      0    CHO     C7      7       0.35     12.011   ;
qtot 0.65
     8       CTL5      0    CHO     C6      8       0.35     12.011   ;
qtot 1

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    1     3     1
    3     4     1
    4     5     1
    5     6     1
    5     7     1
    5     8     1

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     5     1
    2     4     1
    3     6     1
    3     7     1
    3     8     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2
 c3
    2     1     3     5
    1     3     4     5
    3     4     5     5
    4     5     6     5
    4     5     7     5
    4     5     8     5
    6     5     7     5
    6     5     8     5
    7     5     8     5

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2
       c3            c4            c5
    2     1     3     4     9
    1     3     4     5     9
    3     4     5     6     9
    3     4     5     7     9
    3     4     5     8     9

; Include Position restraint file
#ifdef POSRES
#include "posrecholine.itp"
#endif

Now when I include this itp file to the DNA.pdb upto ci and nmol part there
is no problem and I can insert the desired no. of choline molecules in the
system. But when I am calling grompp for the first time, it shows errors
like

too few parameters in the cholineua.itp files,
no defined dihedral,
no bond UB type,
and so on......


Is this because the c0 c1 c2 parameters are not there in my .itp file? If
this is the case, then this .itp file can't be used. So I looked for
Paramchem and Swissparam topology builder which is compatible with CHARMM.
They are known to provide accurate topology parameters. But I dont know how
to use them. The Paramchem requires a .mol2 version of input. But I have
this PDB which is not generating any .str file from Paramchem. There are
certain problem with my university internet connections and all the time I
am not getting connected with these sites. Can anybody provide me a .itp
file for choline molecule which can be used in CHARMM? It may/may not be
based on the pdb file which I am using. I am having difficulties in network
connections and I need this correct choline.itp urgently so that I can
proceed with my project. Alternatively how to tackle the error which I
mentioned while executing GROMPP ? Any kind of help will be hugely
appreciated.

Thanks for your time in advance.
Regards,
Soumadwip Ghosh
Research fellow
Indian Institute of Technology, Bombay
India