[gmx-users] how to construct fatty acid
Tengfei Luo
luotengf at msu.edu
Wed Nov 18 21:04:53 CET 2009
Justin:
Thank you very much! It worked and everything seems reasonable now.
Regards,
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 2:47 PM
Subject: Re: [gmx-users] how to construct fatty acid
>
> When I run grompp using all your files, I get a series of errors:
>
> ERROR 1 [file topol.top, line 60]:
> No default Bond types
>
>
> ERROR 2 [file topol.top, line 144]:
> No default Angle types
>
>
> ERROR 3 [file topol.top, line 190]:
> No default Ryckaert-Bell. types
>
>
> ERROR 4 [file topol.top, line 191]:
> No default Ryckaert-Bell. types
>
> How did you deal with these? The first refers to the OT-HO bond, for
> which there is no known bond type, and the rest are a result of the same
> problematic atom types.
>
> I think you have the carboxylate oxygen types wrong. The carbonyl O
> should be opls_269, and the acid O (in the -OH functional group) should be
> opls_268. These atom types are taken from the ASPH .rtp entry. If you
> switch them, the errors go away and the structure produced seems
> reasonable.
>
> -Justin
>
> Tengfei Luo wrote:
>> 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
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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>>>
>>
>>
>
> --
> ========================================
>
> 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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