Hi,
I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm
using the amber14sb forcefield.
At the top of the top file generated, is an [atomtypes] section. Most of the
atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so
I deleted them however there were two atomtypes A2C and A3C that were not, so I
left them.
Looking back at my files after running some simulations I have realised that
these were meant to be the 2C and 3C atomtypes, which had been converted. I've
also realised that they do not have any mass in the atomtypes section.
---
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
A2C A2C 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91
0.1094
A3C A3C 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91
0.1094
[ moleculetype ]
;name nrexcl
Peptide 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot
bond_type
1 N 1 CYS N 1 -0.415700 14.01000 ; qtot -0.416
2 H 1 CYS H 2 0.271900 1.00800 ; qtot -0.144
3 CX 1 CYS CA 3 0.021300 12.01000 ; qtot -0.123
4 H1 1 CYS HA 4 0.112400 1.00800 ; qtot -0.010
5 A2C 1 CYS CB 5 -0.123100 12.01000 ; qtot -0.133
6 H1 1 CYS HB2 6 0.111200 1.00800 ; qtot -0.022
7 H1 1 CYS HB3 7 0.111200 1.00800 ; qtot 0.089
8 SH 1 CYS SG 8 -0.311900 32.06000 ; qtot -0.223
9 HS 1 CYS HG 9 0.193300 1.00800 ; qtot -0.029
10 C 1 CYS C 10 0.597301 12.01000 ; qtot 0.568
11 O 1 CYS O 11 -0.567901 16.00000 ; qtot -0.000
---
What will this mean for the simulations that I have run?
Kind regards,
James
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