[gmx-users] REGARDING TOPOLOGY FILE

[Subashini .K]

Thank you for the reply.


Have detected the actual problem and fixed it.


The atom numbering is different in mol2 file and hence in the acpype generated file. Nothing wrong in it.


But, in the gro file, apart from two hydrogen atoms and one oxygen atom, there was "EPW".


Hence, had to delete it (which was 415)


Now the .top and .gro match each other.


Simulations are fine.



________________________________
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 12:40 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE

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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