[gmx-users] REGARDING TOPOLOGY FILE

[Amir Zeb]

can you please recognize that two extra atoms generated by acepype??

On Jan 19, 2017 4:00 PM, "Subashini .K" <subashinik at hotmail.com> wrote:

> Thank you very much for the reply.
>
>
> Actually, tried converting the ligand alone to .top and .gro file.
>
>
> The ligand contains only 29 atoms.
>
>
> But, in the top and gro generated by acpype it shows 31 atoms.
>
>
> There lies the problem.
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Amir Zeb <
> zebamir85 at gmail.com>
> Sent: Thursday, January 19, 2017 12:24 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> Hello
> review the number of atoms in gro file and top file
> also check that the 2nd line in gro file showing the total number of atoms
> should be in parallel with all the atoms existed in the gro file
> this way you may solve the problem
> good luck
>
> On Jan 19, 2017 3:20 PM, "Subashini .K" <subashinik at hotmail.com> wrote:
>
> > Hi,
> >
> >
> >
> > Thank you for the reply. As I said earlier, there is one ligand molecule
> > surrounded by many water molecules (680)
> >
> >
> > Here, it is like this
> >
> >
> > [ molecules ]
> > ; Compound        nmols
> >  ligand           1
> >  WAT              680
> >
> >
> > 680 seems to be a correct number. Because, it was computed as follows,
> > using tleap of AMBER TOOLS 15:
> >
> >
> > solvateBox LIG TIP4PBOX 10.0
> >  Solute vdw bounding box:              9.963 8.173 7.953
> >   Total bounding box for atom centers:  29.963 28.173 27.953
> >   Solvent unit box:                     18.860 18.867 18.860
> >   Total vdw box size:                   33.150 30.999 31.097 angstroms.
> >   Volume: 31955.384 A^3
> >   Total mass 12429.154 amu,  Density 0.646 g/cc
> >   Added 680 residues.
> >
> > Still, there is an error.
> >
> >
> > ------------------------------------------------------------
> > ------------------------------------------------------------
> > ------------------------------------------------------------
> > -------------------------------------
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of tasneem
> > kausar <tasneemkausar12 at gmail.com>
> > Sent: Thursday, January 19, 2017 11:04 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
> >
> > The error show that the number of atoms in topology file and gro file
> does
> > not match
> > In last line of topology file define the ligand molecule.
> > here is the exapmle
> >
> > [ molecules ]
> > ; Compound        #mols
> > Protein_chain_A     1
> > DRG                 1
> >
> >
> >
> >
> > On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashinik at hotmail.com>
> > wrote:
> >
> > > Hi gromacs users,
> > >
> > >
> > > Had taken one organic molecule (ligand) and many water molecules using
> > > tleap of Amber tools 15.
> > >
> > >
> > > Then generated .top and .gro file using acpype by the command,
> > >
> > > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> > >
> > >
> > > However, while using the same for gromacs, obtained the following error
> > >
> > >
> > > number of coordinates in coordinate file (conf.gro, 2751)
> > >              does not match topology (topol.top, 2071)
> > >
> > > How to fix this error?
> > >
> > > Thanks,
> > > Subashini.K
> >
> > --
>
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