[gmx-users] how to construct fatty acid

[Tengfei Luo]

Dear All:

I'm new to Gromacs. I want to simulate water disolve in fatty acid 
(C-C-COOH) using a all atom model. I started up with constructing the pdb 
file of decanoic acid. Following the post by Justin 
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added 
the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the 
following [COOH] section into this file

; cooh
[ COOH ]
  [ atoms ]
    C1    opls_136    -0.120    1
    H11   opls_140     0.060    1
    H12   opls_140     0.060    1
    C2    opls_267     0.52     2
    O     opls_268    -0.530    2
    OT    opls_269    -0.44     2
    HO    opls_270     0.45     2
  [ bonds ]
    C1    -C2
    C1    H11
    C1    H12
    C1    C2
    C2    O
    C2    OT
    OT    HO
  [ impropers ]
    C1  OT C2  O   improper_O_C_X_Y

The following lines are also added to the .hdb file inaddition to those 
suggested in the aformentioned link

COOH   2
2      6      H1     C1     C2     -C2
1      2      HO     OT     C2     C1

My pdb file is

ATOM      1  C1  EthB    1       1.000   1.540   0.000
ATOM      2  C2  EthB    1       2.456   2.041   0.000
ATOM      3  C1  Eth     2       2.456   3.581   0.000
ATOM      4  C2  Eth     2       3.912   4.083   0.000
ATOM      5  C1  COOH    3       3.912   5.623   0.000
ATOM      6  C2  COOH    3       5.368   6.124   0.000
ATOM      7  O   COOH    3       6.800   6.124   0.000
ATOM      8  OT  COOH    3       5.300   7.600   0.000
END

I successfully constructed the .top file using pdb2gmx. However, when doing 
minimization, I found that the H attached to the O get too close to this O 
atom. I notice that there is no bond between these two atoms in the top file 
(a part of the top file is attached as follow):

;
; File 'acid.top' was generated
; By user: luotengf (482685)
; On host: dev-intel07
; At date: Tue Nov 17 18:38:45 2009
;
; This is your topology file
; "Drugs are Bad, mmokay" (South Park)
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB 
chargeB      massB
     1   opls_135      1   EthB     C1      1      -0.18     12.011   ; 
qtot -0.18
     2   opls_140      1   EthB    H11      1       0.06      1.008   ; 
qtot -0.12
     3   opls_140      1   EthB    H12      1       0.06      1.008   ; 
qtot -0.06
     4   opls_140      1   EthB    H13      1       0.06      1.008   ; qtot 
0
     5   opls_136      1   EthB     C2      2      -0.12     12.011   ; 
qtot -0.12
     6   opls_140      1   EthB    H21      2       0.06      1.008   ; 
qtot -0.06
     7   opls_140      1   EthB    H22      2       0.06      1.008   ; qtot 
0
     8   opls_136      2    Eth     C1      3      -0.12     12.011   ; 
qtot -0.12
     9   opls_140      2    Eth    H11      3       0.06      1.008   ; 
qtot -0.06
    10   opls_140      2    Eth    H12      3       0.06      1.008   ; qtot 
0
    11   opls_136      2    Eth     C2      4      -0.12     12.011   ; 
qtot -0.12
    12   opls_140      2    Eth    H21      4       0.06      1.008   ; 
qtot -0.06
    13   opls_140      2    Eth    H22      4       0.06      1.008   ; qtot 
0
    14   opls_136      3   COOH     C1      5      -0.12     12.011   ; 
qtot -0.12
    15   opls_140      3   COOH    H11      5       0.06      1.008   ; 
qtot -0.06
    16   opls_140      3   COOH    H12      5       0.06      1.008   ; qtot 
0
    17   opls_267      3   COOH     C2      6       0.52     12.011   ; qtot 
0.52
    18   opls_268      3   COOH      O      6      -0.53    15.9994   ; 
qtot -0.01
    19   opls_269      3   COOH     OT      6      -0.44    15.9994   ; 
qtot -0.45
    20   opls_270      3   COOH     HO      6       0.45      1.008   ; qtot 
0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    1     3     1
    1     4     1
    1     5     1
    5     6     1
    5     7     1
    5     8     1
    8     9     1
    8    10     1
    8    11     1
   11    12     1
   11    13     1
   11    14     1
   14    15     1
   14    16     1
   14    17     1
   17    18     1
   17    19     1

Do you see what is wrong with my approach? I also know there is -ter which 
can replace the end with COOH, but how can I construct the termini to be 
replace at the first place?

I tried to make myself as clear as possible and make the email short. I 
shall appreciate any help or suggestion.

Sincerely,

Tengfei