[gmx-users] adding a new residue type

[Banafsheh Mehrazma]

 Dear all;
I have used a modified guanine in my simulation before, with new parameters
added in amber99 force field and there was no error through the whole
simulation. now I'm trying to do a simulation with modified Guanine on a
different sequence of the DNA with the same commands;
                    pdb2gmx -f modified.pdb -o DNA.gro
                     editconf -f DNA.gro -o DNA_newbox.gro -c -d 1.0 -bt
cubic
                     genbox -cp DNA_newbox.gro -cs spc216.gro -o
DNA_solv.gro -p topol.top
but when I run this one;
                     grompp -f ions.mdp -c DNA_solv.gro -p topol.top -o
ions.tpr
 there is this error
                ERROR  [file topol_DNA_chain_A.itp, line 2304]:
                No default Angle types
so when I checked the topology files,  I saw that for the next residue
after the modified guanine, the O3' has a H3T (bonded to H terminal, which
I don't know where this did came from) and another bond to P of modified
guanine (which should have).  I guess, gromacs recognized it as a terminal
base, however it has the linkage to the next base, as well.

The only difference between my last dna and this one, is that in the last
one the modification was in the 2nd position but this one is in the fourth.

I think there may be a problem with my specbond.dat :
.................................................................................................................................
9
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 1 HEM FE 2 0.25 CYS2 HEME
CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
MET SD 1 HEM FE 1 0.24 MET HEME
CO      C       1       HEME    FE      1       0.19    CO      HEME
CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
8OG P 2 DT O3' 2 0.161 8OG DT
...................................................................................................................................
or maybe not. Any suggestions will be really appreciated. :)

Best regards;
Banafsheh
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