[gmx-users] how to construct fatty acid

Wed Nov 18 20:37:43 CET 2009

Here it is:

title = acid
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIBLE ; use flexible water model
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

Thank you again!

Tengfei

----- Original Message ----- 
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Sent: Wednesday, November 18, 2009 2:34 PM
Subject: Re: [gmx-users] how to construct fatty acid

>
>
> 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
>
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
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