[gmx-users] adding a new residue type

[Mark Abraham]

On 28/02/12, Banafsheh Mehrazma <bmehrazma at gmail.com> 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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