[gmx-users] REGARDING TOPOLOGY FILE

[tasneem kausar]

In topology file the name of ligand defined in  [ moleculetype ] section
and at the end of file as [ molecules ]
 should be same.
Hope this will help you.

On Thu, Jan 19, 2017 at 11:50 AM, 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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