[gmx-users] ACE patch for CHARMM27

[Justin A. Lemkul]

Krzysztof Kuczera wrote:
> 
>  Dear Justin,
> Thank you very much for your quick response, which put me on the right 
> track.
> Of course, I have some more questions and comments.
> 
> 1. Putting residues in .rtp means adding ACE to the peptide sequence.
> This is not the CHARMM convention, where all blocking groups are handled
> through patches to existing residues. The advantage of the .rtp route is 
> that this makes the treatment consistent with the other implemented 
> force fields.
> 

There has been some discussion about implementing such complex patching 
capabilities in Gromacs, but as of yet, there is no progress publicly 
implemented.  For this reason, it is easiest to simply construct the capping 
groups yourself.

> 2. I believe the residues from the email need a little tweaking for 
> consistency with CHARMM topology/parameters.
> 

Perhaps; I can't comment on any of that.

> [ ACE ] needs an extra improper and a CMAP term:
> [ impropers ]
> +N CH3 CA +HN
> [ cmap ]
> C +N +CA +C
> 
> and [ NAC ] needs a CMAP term
> [ cmap ]
> -N  -CA  -C  N
> 
> 3. Why won't the .n.tdb approach work?
> The other reason I went with the .n.tdb file was that the amide (CT2) and
> N-methylamide (CT3) C-terminals are already implemented in the .c.tdb
> (CT3 is equivalent to the emailed NAC, with CMAP included). Belatedly,
> I see that the authors of CT3 also had problems with missing bonds, and 
> added
> one in explicitly - I will try that and check my .top file for energy 
> terms.
> 

The terminal patching capacity is somewhat limited in its elegance.  Finding and 
replacing an atom or two at a time is fairly simply, but constructing an entire 
"residue" is not something the code can likely handle in its current incarnation.

-Justin

> Thanks
> Krzysztof
> 
> On 9/17/10 5:14 PM, Justin A. Lemkul wrote:
>>
>>
>> Krzysztof Kuczera wrote:
>>>  Hi GMXers,
>>>
>>> I am interested in simulating blocked peptides with CHARMM (and other
>>> force fields), using gromacs-4.5, and would appreciate some help from
>>> more experienced GROMACS users on details.
>>>
>>> To test things out I made a stab at creating an ACE N-terminal patch 
>>> - this exists in OPLSAA, AMBER and CHARMM, so I added this to 
>>> charmm27.ff/aminoacids.n.tdb:
>>>
>>> [ ACE ]
>>> [ add ]
>>>  1     2     CY   N    CA   C
>>>        C    12.01100    0.51
>>>  1     2     OY   CY   N    CA
>>>        O    15.99900   -0.51
>>>  1     1     CAY  CY   OY   N
>>>        CT3  12.01100  -0.27
>>>  3     4     HY   CAY  CY   N
>>>        HA    1.00800   0.09
>>> [ impropers ]
>>>  CY CAY N OY
>>>  N  CY  CA HN
>>> [ cmap ]
>>>  CY  N  CA  C  +N
>>>
>>>
>>> Then built the top file with:
>>> pdb2gmx -f -inter ala5_alpha.pdb -p ala5.top -o ala5.gro -ff charmm27 
>>> -water tip3p -nochargegrp
>>>
>>> selecting ACE/CT2 as my terminal types
>>>
>>>
>>> The ala5.gro geometry looks fine, but in the ala5.top file  there is 
>>> no bond between atoms 2 and 7 (CY==OY in the patch), so the OY oxygen 
>>> starts to drift off in EM and MD. All other bonds are generated.
>>>
>>> Can you tell me what is wrong here? Maybe somebody has already made a
>>> patch that works?
>>>
>>
>> Nowhere in the .tdb entry is such a bond specified, nor can it be.  
>> The correct approach is to define .rtp entries, i.e.:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2010-July/052270.html
>>
>> -Justin
>>
>>> I attach the ala5_alpha.pdb file
>>>
>>> Krzysztof
>>>
>>
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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