On 3/14/20 1:59 AM, Billy Williams-Noonan wrote:
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
C1CL0.542 2
C2CA -0.280 3
H2R HAL20.090 4
H2S HAL20.090 5
C3 CTL2 -0.180 6
H3R HAL20.090 7
H3S HAL20.090 8
C4 CTL2 -0.180 9
H4R HAL20.090 10
H4S HAL20.090 11
C5 CTL2 -0.180 12
H5R HAL20.090 13
H5S HAL20.090 14
C6 CTL2 -0.180 15
H6R HAL20.090 16
H6S HAL20.090 17
C7 CTL2 -0.180 18
H7R HAL20.090 19
H7S HAL20.090 20
C8 CTL2 -0.180 21
H8R HAL20.090 22
H8S HAL20.090 23
C9 CTL2 -0.180 24
H9R HAL20.090 25
H9S HAL20.090 26
C10 CTL2 -0.180 27
H10R HAL20.090 28
H10S HAL20.090 29
C11 CTL2 -0.180 30
H11R HAL20.090 31
H11S HAL20.090 32
C12 CTL2 -0.180 33
H12R HAL20.090 34
H12S HAL20.090 35
C13 CTL2 -0.180 36
H13R HAL20.090 37
H13S HAL20.090 38
C14 CTL3 -0.270 39
H14R HAL30.090 40
H14S HAL30.090 41
H14T HAL30.090 42
[ bonds ]
O1C1
C1C2
C1+N
C2 H2R
C2 H2S
C2C3
C3 H3R
C3 H3S
C3C4
C4 H4R
C4 H4S
C4C5
C5 H5R
C5 H5S
C5C6
C6 H6R
C6 H6S
C6C7
C7 H7R
C7 H7S
C7C8
C8 H8R
C8 H8S
C8C9
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+NC 9 0.00 7.531200 1
C2 C1+N HN 9 0.00 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?
The issue comes from whatever the amino acid is; the [impropers] and
[cmap] entries specify that -C is needed to impose these bonded
interactions. Your MYR residue does not have
