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

[Justin Lemkul]

On 1/10/17 4:49 AM, Tushar Ranjan Moharana wrote:
> 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.
>

Given that serine and fatty acids already exist in CHARMM, you only need to work 
with the linker (presumably an ester).  There are some parameters for such 
species already in CHARMM so you should look to see what's available already, 
and then proceed with parametrizing, e.g. methylacetate and building the rest of 
the residue from stock building blocks.

-Justin

> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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