[gmx-users] how to construct fatty acid
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 18 20:47:38 CET 2009
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
>>>>
>>>> ========================================
>>>> --
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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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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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
========================================
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