Dear Jason,
Thank you very much for your reply.
The problem has been solved according to your suggestions.
I modified the atom name and residue name of Cl- according to the format in
pdbxyz.f, and it works.
...
ATOM 2459 OXT GLY 153 -17.901 4.475 -11.067 1.00 0.00
TER
HETATM 2460 CL CL 154 -0.396 16.562 -0.070 1.00 0.00
TER
HETATM 2461 CL CL 155 -14.052 -6.988 7.849 1.00 0.00
...
Thank you very much.
Best regards,
Ya Gao
On Tue, Dec 9, 2014 at 2:00 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, 2014-12-09 at 00:47 +0800, Ya Gao wrote:
> > Dear all,
> >
> > I want to perform a simulation with amoebapro13 force field and amoeba
> > water model using pmemd.amoeba in amber14.
> >
> > The system is myoglobin, which is placed in a cubic water box using
> > solvatebox with 2 Cl- ions to neutralize the system.
> >
> > The correct pdb.xyz file can be generated using pdbxyz.x in tinker-6.3.3.
> >
> > However, when I move to the next step to generate the .analout file,
> there
> > is a error and couldn't generate the correct .analout file.
> >
> > I checked the input and output files carefully, and found that the error
> is
> > caused due to the Cl- ions.
> >
> > I tested to remove the ions from the pdb file, and the corresponding
> > correct .analout file can be generated.
> >
> > So can anybody give me some help in dealing with the system with ions
> using
> > tinker ?
>
> Tinker _should_ recognize ions. If you look at amoebapro13.prm, you'll
> see the following lines:
>
> atom 255 51 Mg+ "Magnesium Ion Mg+2" 12 24.305
> 0
> atom 256 52 Ca+ "Calcium Ion Ca+2" 20 40.078
> 0
> atom 257 53 Zn+ "Zinc Ion Zn+2" 30 65.390
> 0
> atom 258 54 Cl- "Chloride Ion Cl-" 17 35.453
> 0
>
> and then again at the bottom:
>
> biotype 2004 K "Potassium Ion" 251
> biotype 2005 MG "Magnesium Ion" 255
> biotype 2006 CA "Calcium Ion" 256
> biotype 2007 CL "Chloride Ion" 258
>
> What I suspect is happening is that the Chloride atom type isn't named
> correctly for Tinker to recognize it. Try experimenting with different
> names for the chlorine residue and atoms, like Cl- and CL (I'm not quite
> sure what tinker uses the "biotype" vs. "atom" records for), and perhaps
> with different justifications (e.g., left-justified in the 4-letter
> space assigned for atom and residue names).
>
> If you are still having trouble, can you send me your files off-list so
> I can take a look? The easier you make it for me to reproduce your
> problem, the faster I will be able to help debug.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
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Received on Mon Dec 08 2014 - 22:00:02 PST
