[gmx-users] Re: adding a new residue type

[Banafsheh Mehrazma]

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 <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. :)
>
> Best regards;
> Banafsheh
>
>
>
>
>
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