[gmx-users] Linking MYR residue to N-terminus using pdb2gmx

[Billy Williams-Noonan]

Hi Experts,

This is a long-ish e-mail so thank you very much for your time

I am using the GROMACS compatible charmm36 forcefield for
betapeptides described here:
https://gitlab.com/awacha/charmm-beta.ff

In merged.rtp I have redefined the MYR residue hoping I could link it to
the N-terminus of my b-peptide


[ MYR ]
  [ atoms ]
           O1   OCL   -0.546  1
           C1    CL    0.542  2
           C2    CA   -0.280  3
          H2R  HAL2    0.090  4
          H2S  HAL2    0.090  5
           C3  CTL2   -0.180  6
          H3R  HAL2    0.090  7
          H3S  HAL2    0.090  8
           C4  CTL2   -0.180  9
          H4R  HAL2    0.090 10
          H4S  HAL2    0.090 11
           C5  CTL2   -0.180 12
          H5R  HAL2    0.090 13
          H5S  HAL2    0.090 14
           C6  CTL2   -0.180 15
          H6R  HAL2    0.090 16
          H6S  HAL2    0.090 17
           C7  CTL2   -0.180 18
          H7R  HAL2    0.090 19
          H7S  HAL2    0.090 20
           C8  CTL2   -0.180 21
          H8R  HAL2    0.090 22
          H8S  HAL2    0.090 23
           C9  CTL2   -0.180 24
          H9R  HAL2    0.090 25
          H9S  HAL2    0.090 26
          C10  CTL2   -0.180 27
         H10R  HAL2    0.090 28
         H10S  HAL2    0.090 29
          C11  CTL2   -0.180 30
         H11R  HAL2    0.090 31
         H11S  HAL2    0.090 32
          C12  CTL2   -0.180 33
         H12R  HAL2    0.090 34
         H12S  HAL2    0.090 35
          C13  CTL2   -0.180 36
         H13R  HAL2    0.090 37
         H13S  HAL2    0.090 38
          C14  CTL3   -0.270 39
         H14R  HAL3    0.090 40
         H14S  HAL3    0.090 41
         H14T  HAL3    0.090 42
  [ bonds ]
           O1    C1
           C1    C2
           C1    +N
           C2   H2R
           C2   H2S
           C2    C3
           C3   H3R
           C3   H3S
           C3    C4
           C4   H4R
           C4   H4S
           C4    C5
           C5   H5R
           C5   H5S
           C5    C6
           C6   H6R
           C6   H6S
           C6    C7
           C7   H7R
           C7   H7S
           C7    C8
           C8   H8R
           C8   H8S
           C8    C9
           C9   H9R
           C9   H9S
           C9   C10
          C10  H10R
          C10  H10S
          C10   C11
          C11  H11R
          C11  H11S
          C11   C12
          C12  H12R
          C12  H12S
          C12   C13
          C13  H13R
          C13  H13S
          C13   C14
          C14  H14R
          C14  H14S
          C14  H14T
  [ impropers ]
            C1   C2    +N     O1


In ffnonbonded.itp I have added the following dihedral types:

     C2       C1        +N        C     9     0.000000     7.531200     1
     C2       C1        +N       HN     9     0.000000     7.531200     1




Running pdb2gmx I get the following error:

*gmx pdb2gmx -f outpdb.pdb -o pep.pdb -p pep.top -ter*

Processing chain 1 'A' (105 atoms, 4 residues)
Identified residue MYR1 as a starting terminus.
Identified residue B3K4 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for MYR-1
 0: Beta3NH3+
 1: Beta2NH3+
 2: Beta23NH3+
 3: B3_NH2
 4: B2_NH2
 5: B23_NH2
 6: 5TER
 7: None
7
Start terminus MYR-1: None
Select end terminus type for B3K-4
 0: BetaCOO-
 1: BetaCOOH
 2: BetaCT2
 3: 3TER
 4: None
0
End terminus B3K-4: BetaCOO-
Opening force field file ./charmm36_betapep.ff/betaaminoacids.arn
Opening force field file ./charmm36_betapep.ff/cyclicbeta.arn
Opening force field file ./charmm36_betapep.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 4 residues with 106 atoms
Making bonds...
Number of bonds was 105, now 105
Generating angles, dihedrals and pairs...
Before cleaning: 288 pairs

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2018.2
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 148)

Fatal error:
Residue 2 named MYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

It seems to be having a problem recognising the link between C1 of Myr and
the N-terminus of the next residue (B3K) - is there a file where I can
explicitly mention this?

Any help would be appreciated - how do I fix this?

Cheers,
Billy
-- 
Billy Noonan*    |    *Postdoctoral Research Fellow    *|*    Bsci ( *Adv*
), IA Hon

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