[gmx-users] how to construct fatty acid

[Justin A. Lemkul]

Tengfei Luo wrote:
> 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):
> 

Does the bond length change somehow?  Or does the H get close to the carbonyl 
oxygen in the -COOH group?  Are you doing the minimization in vacuo?  If so, the 
strong (condensed-phase) charges that you have assigned may be inappropriate in 
the absence of solvent, which will screen electrostatic effects.

<snip>

The topology looks reasonable.

> 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?
> 

The -ter option does not function for non-protein compounds, as stated in the 
thread you cite.

-Justin

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

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================