On 28/02/12, Banafsheh Mehrazma <[email protected]> wrote: > > 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. :) > >
We don't have enough information to suggest anything. If the only difference really is the order of non-terminal amino acids, then your symptoms seem impossible. You should look at line 2304 and work backwards. Mark
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