[gmx-users] ACE patch for CHARMM27

[Justin A. Lemkul]

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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