What about OHN - the hydroxyl radical? I put two of them in the system to
understand the issue. Under DNA_chain_X, you clearly see nr=2 for OHN. If I
take one OHN out from pdb (means one DTMP, one OHN and water), I again get
nr=1 for OHN.
residue (2):
> residue[0]={name="DTMP", nr=1, ic=' '}
> residue[1]={name="OHN", nr=2, ic=' '}
Pradip
On Tue, Aug 20, 2013 at 3:12 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote:
> residue is a sub-field of moltype, so you are seeing that there is
> indeed one SOL residue per water molecule, as expected. Look elsewhere
> and you will see that there are 351 of those molecules recorded. The
> same is true of the DNA chain, but since there's only one DNA chain,
> the number of residues per molecule coincides with the number in the
> system.
>
> Mark
>
> On Tue, Aug 20, 2013 at 7:48 PM, Pradip Biswas <biswas...@gmail.com>
> wrote:
> > Hi,
> >
> > I am using v-4.5.5. I have a system of DNA nucleotide & *two* OH radicals
> > solvated in water.
> >
> > The topology file has the following records in the end:
> >
> > [ molecules ]
> > ; Compound #mols
> > DNA_chain_X 1
> > SOL 351
> >
> >
> > However, when I did gmxdump after running grompp, I see the following:
> >
> > moltype (0):
> > name="DNA_chain_X"
> > ...............
> > ...............
> > residue (2):
> > residue[0]={name="DTMP", nr=1, ic=' '}
> > residue[1]={name="OHN", nr=2, ic=' '}
> >
> >
> > moltype (1):
> > name="SOL"
> > ..........
> > ..........
> > residue (1):
> > residue[0]={name="SOL", *nr=1*, ic=' '}
> >
> > Aren't we recording the number of solvent residues? I was expecting
> nr=351
> > for SOL; the number of water molecule I have in the system. As I get nr=2
> > for OHN
> >
> > Thanks,
> > Pradip Biswas
> >
> >
> >
> > --
> > P. K. Biswas, PhD
> > Laboratory of Computational Biophysics & Bioengineering
> > Associate Professor of Physics
> > Tougaloo College
> > 601-977-7788
> > --
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--
P. K. Biswas, PhD
Laboratory of Computational Biophysics & Bioengineering
Associate Professor of Physics
Tougaloo College
601-977-7788
--
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