[gmx-users] dialanine using charmm27 ff

[Mark Abraham]

On 9/09/2011 8:05 AM, Sandeep Somani wrote:
> Hi
>
> I am trying to set up a simulation for dialanine using charmm27 ff but 
> am getting errors in pdb2gmx due to missing definitions in rtp file.
>
> I created the pdb file (below) using Charmm for the sequence 
> ACE-ALA-ALA-CT3.
>
> pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE 
> and CT3.

Yes, CHARMM in GROMACS has lacked these for some time. I asked over a 
year ago for them to be added, but that hasn't happened. You can add

[ ACE ]
  [ atoms ]
         CT3     CT3     -0.270  0
         HT1     HA      0.090   1
         HT2     HA      0.090   2
         HT3     HA      0.090   3
         C       C       0.510   4
         O       O       -0.510  5
  [ bonds ]
         C       CT3
         C       +N
         CT3     HT31
         CT3     HT32
         CT3     HT33
         O       C
  [ impropers ]
         C       CT3     +N      O

[ CT3 ]
; this can also be done with the .c.tdb, but the atom naming is different
; and this can matter
  [ atoms ]
         N       NH1     -0.470  0
         HN      H       0.310   1
         CT      CT3     -0.110  2
         HT1     HA      0.090   3
         HT2     HA      0.090   4
         HT3     HA      0.090   5
  [ bonds ]
         -C      N
         N       HN
         N       CAT
         CT      HT1
         CT      HT2
         CT      HT3

  [ impropers ]
         N       -C      CAT     HN
         -C      CAT     N       -O

to the end of aminoacids.rtp in a local copy of the charmm27.ff folder 
to make this work.

>
> Does someone have the appropriate definitions for these residues ?
> ( I have tried http://swissparam.ch/ to generate an itp file for the 
> molecule, but upon using it in GMX it does not give the same energy as 
> that from charmm. )

That will likely be a separate issue.

Mark