[gmx-users] Adding a new(modefied) fatty acid to charm 36 force field.

[Tushar Ranjan Moharana]

Hi All,
I want to understand the interaction of a fatty acid to various amino acid
side chain while it forms a covalent link with the hydroxyle group of the
serine. For that I wanted to add covalently linked serine-fatty acid as a
different amino acid so the pdb2gmx can generate the topology. For the
above reason I made the required complex in pdb format and converted to
mol2 format and generated .itp file from swissparam server. My plan was to
copy the [ atom ]  and [ bond ] section of the .itp to aminoacid.rtp under
the new amino acid with suitable modifications and add it to
residuetype.dat with type protein.

While trying the above, I did the same thing with only serine
(unmodefied).  The [ atom ] and [ bond ] section of the .itp generated by
swissparam looks completly different from that of serine mentioned in
aminoacid.rtp. This is giving me a fishy smell about what I am doing.
Kindly enlighten me about my mistakes and the correct protocol to do the
same. Following are the entry of  the [ atom ] and [ bond ] section of the
aminoacid.rtp and .itp that I have generated.

aminoacid.rtp entry

[ SER ]
 [ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 0.05 4
HB1 HA 0.09 5
HB2 HA 0.09 6
OG OH1 -0.66 7
HG1 H 0.43 8
C C 0.51 9
O O -0.51 10
 [ bonds ]
CB CA
OG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
OG HG1
O C
 [ impropers ]
N -C CA HN
C CA +N O
 [ cmap ]
-C N CA C +N


Modifiedserine.itp entry


[ atoms ]
; nr type resnr resid atom cgnr charge mass
   1 CR   1 MSER CA      1  0.3310  12.0110
   2 C=O  1 MSER C       2  0.6590  12.0110
   3 O=C  1 MSER O       3 -0.5700  15.9994
   4 CR   1 MSER CB      4  0.2800  12.0110
   5 NR   1 MSER N01     5 -0.9900  14.0067
   6 OR   1 MSER O01     6 -0.6500  15.9994
   7 OR   1 MSER O02     7 -0.6800  15.9994
   8 HOCO 1 MSER H01     8  0.5000   1.0079
   9 HNR  1 MSER H02     9  0.3600   1.0079
  10 HCMM 1 MSER H03    10  0.0000   1.0079
  11 HCMM 1 MSER H04    11  0.0000   1.0079
  12 HCMM 1 MSER H05    12  0.0000   1.0079
  13 HNR  1 MSER H06    13  0.3600   1.0079
  14 HOR  1 MSER H07    14  0.4000   1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
  8   6 1 0.09810  445818.6  0.09810  445818.6
 11   4 1 0.10930  287014.9  0.10930  287014.9
  9   5 1 0.10190  390836.6  0.10190  390836.6
  6   2 1 0.13550  349343.9  0.13550  349343.9
 14   7 1 0.09720  469365.3  0.09720  469365.3
  4  12 1 0.10930  287014.9  0.10930  287014.9
  4   7 1 0.14180  303937.5  0.14180  303937.5
  4   1 1 0.15080  256422.3  0.15080  256422.3
  2   3 1 0.12220  779866.6  0.12220  779866.6
  2   1 1 0.14920  252327.8  0.14920  252327.8
  5  13 1 0.10190  390836.6  0.10190  390836.6
  5   1 1 0.14510  306165.0  0.14510  306165.0
  1  10 1 0.10930  287014.9  0.10930  287014.9

-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB