[gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)

Fri Jun 24 00:34:16 CEST 2016

Hi Mark,

   I noticed your paper from 2011 on parameter optimisation using EWALD and
your position and GROMACS so I feel humbled to be talking with you.

   I have had a 'guess' at the topology for b-alanine (BAL) and added it to
my aminoacids.rtp file in the gromos forcefield directory that I am using.
My guess is based on the parameters for alanine, and I am assuming that
what I have done would not be viable if two BAL residues were directly next
to each other.  Is what I have done correct and would it work?

;beta-alanine

[ BAL ]
 [ atoms ]
    N     N    -0.3100      0
    H     H     0.3100      0
   CA   CH2     0.0000      1
   CB   CH2     0.0000      1
    C     C     0.4500      2
    O     O    -0.4500      2
 [ bonds ]
    N     H    gb_2
    N    CA    gb_21
   CA    CB    gb_27
   CB     C    gb_27
    C     O    gb_5
    C    +N    gb_10
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_32
   -C     N    CA     ga_31
    H     N    CA     ga_18
    N    CA    CB     ga_13
   CA    CB     C     ga_13
   CB     C     O     ga_30
   CB     C    +N     ga_19
    O     C    +N     ga_33
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
   CA     N     C    CB     gi_2
    C    CB    +N     O     gi_1
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_14
   -C     N    CA    CB     gd_44
   -C     N    CA    CB     gd_43
   CA    CB     C    +N     gd_45
   CA    CB     C    +N     gd_42

When I run the command gmx pdb2gmx it gives me the following error:

Fatal error:
Atom OXT in residue BAL 7 was not found in rtp entry BAL with 6 atoms
while sorting atoms.

Additionally, it tells me this before the error message, while processing
the command:

Opening force field file ./gromos54a7_atb.ff/aminoacids.r2b
Reading sim_lig_1.pdb...
Read 60 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 7 residues with 60 atoms

  chain  #res #atoms
  1 'C'     7     60

All occupancies are one
Opening force field file ./gromos54a7_atb.ff/atomtypes.atp
Atomtype 63
Reading residue database... (gromos54a7_atb)
Opening force field file ./gromos54a7_atb.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 109
Sorting it all out...
Opening force field file ./gromos54a7_atb.ff/aminoacids.hdb
Opening force field file ./gromos54a7_atb.ff/aminoacids.n.tdb
Opening force field file ./gromos54a7_atb.ff/aminoacids.c.tdb
Processing chain 1 'C' (60 atoms, 7 residues)
Identified residue TRP1 as a starting terminus.
Warning: Residue BAL7 in chain has different type (Other) from starting
residue TRP1 (Protein).
Identified residue ASN6 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus TRP-1: NH3+
End terminus ASN-6: COO-

Apologies for the ignorance, but do you know what I need to do to fix this?

Billy

On 23 June 2016 at 17:44, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> There's a collection of contributed stuff on the GROMACS webpage, so good
> luck with that... But mostly it's a matter of people choosing to share.
> Authors of papers where such have been used should be willing to share
> topology files.
>
> Mark
>
> On Thu, Jun 23, 2016 at 8:08 AM Billy Williams-Noonan <
> billy.williams-noonan at monash.edu> wrote:
>
> > Hi Gromacs Users,
> >
> >   Does anyone know where I can find a set of download-able parameters for
> > rare amino acids?  Is there a repository of some kind?
> >
> > Kind regards,
> >
> > Billy
> >
> > --
> > Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
> >
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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052