[gmx-users] tip4p2005 with gromacs 4.6.5
jalemkul at vt.edu
Thu Feb 18 14:36:58 CET 2016
On 2/17/16 6:29 PM, Irem Altan wrote:
> Thanks! It solved most of the problem.
> I am now getting an error during energy minimization:
> The [molecules] section of your topology specifies more than one block of
> a [moleculetype] with a [settles] block. Only one such is allowed. If you
> are trying to partition your solvent into different *groups* (e.g. for
> freezing, T-coupling, etc.) then you are using the wrong approach. Index
> files specify groups. Otherwise, you may wish to change the least-used
> block of molecules with SETTLE constraints into 3 normal constraints.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I am in fact labeling water molecules separately, but this had worked before with TIP4P.
> my topology file looks like this:
> ; Include forcefield parameters
> #include "./amber99sb.ff/forcefield.itp"
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Other_chain_A2.itp"
> #include "topol_Other_chain_B2.itp"
> ; Include water topology
> #include "./amber99sb.ff/tip4p2005.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> ; Include topology for ions
> #include "./amber99sb.ff/ions.itp"
> #include "./tip4p2005cw.itp"
> [ system ]
> ; Name
> Protein in water
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> Other_chain_A2 1
> Other_chain_B2 1
> HO4 96
> HO4 62
> SOL 5763
> NA 6
> CL 10
> where tip4p2005cw.itp has the molecule name defined as HO4:
> [ moleculetype ]
> ; molname nrexcl
> HO4 2
> Does this somehow clash with TIP4P’s HO4? Do I need to name it differently?
From the error message:
"The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed."
You cannot have [settles] in more than one topology. If you're defining
different water types, you have to do as the error message tells you and
re-formulate the constraints.
> On Feb 17, 2016, at 5:48 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
> On 2/17/16 5:41 PM, Irem Altan wrote:
> I would like to use TIP4P2005 with Gromacs 4.6.5 for a protein simulation with water. I have the .itp and .gro files for the model.
> I am using a slightly modified version of the Amber forcefields, so I have a folder called amber99sb.ff in my working directory. I have added a file called tip4p2005.itp into that folder. I then tried the following:
> pdb2gmx -f amber99sb.ff/ -water tip4p2005.itp -o box.gro -p topol.top
> as well as
> pdb2gmx -f amber99sb.ff/ -water tip4p2005 -o box.gro -p topol.top
> both of which result in an error saying “invalid argument tip4p2005(.itp) for option -water”.
> How can I get this to work?
> It must match the first field of an entry in watermodels.dat in the force field directory.
> Also note that pdb2gmx -f takes a coordinate file, not a directory name. That will cause a whole host of failures...
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> Gromacs Users mailing list
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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