[gmx-users] regarding pdb2gmx

[soumadwip ghosh]

Hi all,
        I have a general query about the basic functioning of pdb2gmx. I
recently observed that when I take a PDB file for a DNA molecule and build
its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
without any hitches. If I look at the .itp file made for the DNA chain it
looks like,

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
; residue   1 DC  rtp DC   q -0.5
     1        ON5      1     DC    O5'      1      -0.66    15.9994   ;
qtot -0.66
     2        HN5      1     DC    H5T      2       0.43      1.008   ;
qtot -0.23
     3       CN8B      1     DC    C5'      3       0.05     12.011   ;
qtot -0.18
     4        HN8      1     DC   H5'1      4       0.09      1.008   ;
qtot -0.09
     5        HN8      1     DC   H5'2      5       0.09      1.008   ;
qtot 0
     6        CN7      1     DC    C4'      6       0.16     12.011   ;
qtot 0.16
     7        HN7      1     DC    H4'      7       0.09      1.008   ;
qtot 0.25
     8        ON6      1     DC    O4'      8       -0.5    15.9994   ;
qtot -0.25
     9       CN7B      1     DC    C1'      9       0.16     12.011   ;
qtot -0.09
    10        HN7      1     DC    H1'     10       0.09      1.008   ;
qtot 0
    11        NN2      1     DC     N1     11      -0.13     14.007   ;
qtot -0.13
    12        CN3      1     DC     C6     12       0.05     12.011   ;
qtot -0.08
    13        HN3      1     DC     H6     13       0.17      1.008   ;
qtot 0.09
    14        CN3      1     DC     C5     14      -0.13     12.011   ;
qtot -0.04
    15        HN3      1     DC     H5     15       0.07      1.008   ;
qtot 0.03
    16        CN1      1     DC     C2     16       0.52     12.011   ;
qtot 0.55
    17       ON1C      1     DC     O2     17      -0.49    15.9994   ;
qtot 0.06
    18        NN3      1     DC     N3     18      -0.66     14.007   ;
qtot -0.6
    19        CN2      1     DC     C4     19       0.65     12.011   ;
qtot 0.05
    20        NN1      1     DC     N4     20      -0.75     14.007   ;
qtot -0.7
    21        HN1      1     DC    H41     21       0.37      1.008   ;
qtot -0.33
    22        HN1      1     DC    H42     22       0.33      1.008   ;
qtot 0
    23        CN8      1     DC    C2'     23      -0.18     12.011   ;
qtot -0.18
    24        HN8      1     DC   H2'1     24       0.09      1.008   ;
qtot -0.09
    25        HN8      1     DC   H2'2     25       0.09      1.008   ;
qtot 0
    26        CN7      1     DC    C3'     26       0.01     12.011   ;
qtot 0.01
    27        HN7      1     DC    H3'     27       0.09      1.008   ;
qtot 0.1
    28        ON2      1     DC    O3'     28      -0.57    15.9994   ;
qtot -0.47
For one residue.
However, if you look at the [ bond ] section of this .itp file it looks
like,

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    1     3     1
    3     4     1
    3     5     1
    3     6     1
    6     7     1
    6     8     1
    6    26     1
    8     9     1
    9    10     1
    9    11     1
    9    23     1
   11    12     1
   11    16     1
   12    13     1
There are no parameters in the right and by principle grompp should
complain about this. But the simulation runs fine and the proper
interactions with the desired outcomes are always obtained. However, things
get altered when I proceed to model anything else than a DNA/protein. As
for example, I have made a topology for tetramethyl ammonium ion ( in
CHARMM 27) and as usual it lacks these parameters in all the [ bonds ],
{angle ] or [ dihedral ] sections. I changed the .top extension to tma.itp
and included in the system topology for a double stranded DNA molecule
according to standard protocols. Now when I start grompp it screams about
the 'missing parameters in the tma.itp ffile'. My question is everytime I
model something my CHARMM, do I have to include parameters such as force
constant, phi0, b0, mult etc from the ffbonded.itp file manually or does
pdb2gmx should write it looking at the connectivity mentioned in the PDB
file? The same thing goes for writing sigma and epsilon terms from the
ffnonbonde.itp file manually or pdb2gmx should do it by default? I have
another question that is it ok not to specify the [ atomtypes ] and [
pairtypes ] in the .itp file because without these being specified
properly, is it possible that the correct non bonding interaction arises? I
have always seen SWISSPARAM and ATB topologies come with all these things
mentioned from the scratch but with pdb2gmx I have never seen it. So, is it
like pdb2gmx gives only the atoms making the bonds, angles, prop and
improp. dihedrals (atomtypes already mentioned in the aminoacids.rtp file)
and the rest of the parameters are to placed manually or am i missing
something regarding pdb2gmx( some flags)??
Recently, I wanted to simulate graphene and although the ideal job is to go
with g_x2top, issuing pdb2gmx should also work right? The topology is
getting formed but without the c0, c1, c2...etc parameters. I dig up the
ffbonded and ffnonboned.itp files from the CHARMM27.ff library and have
manually placed them. It no longer shows an error but I'm still not assured
whether the correct interaction would arise or not.

If anyone can spare some of their times and help me understand this I would
be highly obliged. Sorry if I am asking for much.

Soumadwip Ghosh
Research Fellow
IITB
India