[gmx-users] REGARDING TOPOLOGY FILE

[Subashini .K]

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