[gmx-users] how to construct fatty acid

[Tengfei Luo]

Justin:

Thank you for your help!

Yes, the OH bond length changed before and after minimization. and yes, the 
H get close to the carbonyl O in the COOH group. I did the minimization with 
solvent.

I appreciate any further suggestion!

Tengfei

----- Original Message ----- 
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, November 18, 2009 2:21 PM
Subject: Re: [gmx-users] how to construct fatty acid


>
>
> 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
>
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