dear Mark; I forgot to mention that the O3' in the next residue (a native thymine) that is bonded to P in modified base, is changed to atom type OH instead of being OS. However in the dna.rtp file, for [ DT ] O3' is OS, not OH. and the line 2304 is the angle P OH C3', which we don't have in the ffbonded.itp. But we have P OS C3'. I have no idea why the gromacs is reading the O3', OH instead of OS!
Thank you Banafsheh On Tue, Feb 28, 2012 at 12:46 PM, 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. :) > > Best regards; > Banafsheh > > > > >
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