[gmx-users] how to construct fatty acid

[Justin A. Lemkul]

Tengfei Luo wrote:
> 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!

Can you post your .mdp file?  I have never seen any instability in OPLS -COOH 
groups like you've described.

-Justin

> 
> 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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> 
> 

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

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

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