[gmx-users] TIP4P water model

[Justin Lemkul]

On 9/23/12 2:28 PM, Ankita naithani wrote:
> Hi,
>
> So the commands from the beginning are appended below:
>
> pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro
>
> (I choose option 6 for AMBER99sb-ILDN force field and then option 2
> for TIP4P water model)
>
> editconf -f system.gro -o system_box.gro -c -d 1.0 -bt dodecahedron
>
> genbox -cp system_box.gro -cs tip4p.gro -o system_solv.gro -p topol.top
>
> grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
>
> And it is here that I get the error :
>
> Fatal error:
> number of coordinates in coordinate file (system_solv.gro, 421880)
>               does not match topology (topol.top, 416008)
>
> I am appending below the contents of my topology file:
>
> ;
> ;	File 'topol.top' was generated
> ;	By user: onbekend (0)
> ;	On host: onbekend
> ;	At date: Fri Sep 21 14:02:35 2012
> ;
> ;	This is a standalone topology file
> ;
> ;	It was generated using program:
> ;	pdb2gmx_d - VERSION 4.5.5
> ;
> ;	Command line was:
> ;	/usr/local/src/gromacs/bin/pdb2gmx_d -vsite h -f 3HQN_tet-nolig.pdb
> -o system.gro
> ;
> ;	Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_A2.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_B2.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_C2.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_D2.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/tip4p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_A2     1
> Protein_chain_B     1
> Protein_chain_B2     1
> Protein_chain_C     1
> Protein_chain_C2     1
> Protein_chain_D     1
> Protein_chain_D2     1
> SOL               340
> SOL               394
> SOL               340
> SOL               394
> SOL             94333
>
> -------------------------------
>
> I cannot understand as to why it is generating error at this stage. It
> would be really helpful if you could advice me how to proceed from
> here.
>

The difference in the number of atoms (5872) is exactly equal to 4 * (340 + 394 
+ 340 + 394), so the presence of multiple SOL entries is causing a problem. 
Verify that these molecules are indeed in TIP4P form, and if they are (i.e. they 
were correctly constructed in pdb2gmx), try merging the SOL blocks into one 
single entry in the topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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