Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: When I created em.tpr I got the followings notes: *_NOTE 1 [file topol.top, line 52]:_* System has non-zero total charge: -1.50e+01 _*NOTE 2 [file topol.top]:*_ The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geo

Re: [gmx-users] The solvent group Water is not continuous

When I created em.tpr I got the followings notes: *NOTE 1 [file topol.top, line 52]:* System has non-zero total charge: -1.50e+01 *NOTE 2 [file topol.top]:* The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups the

Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: Dear users, I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta. ...and hopefully did a complete re-parameterization of the nonsense charges it gives. http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips That's an aside, completely unrelated

Re: [gmx-users] The solvent group Water is not continuous

Dear users, I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta. genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log select group:13 Fatal error: The solvent group SOL is not continuous: index[984]=5334, index[985]=5355 For more information and tips for troubleshooting, ple

Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: I tried SOL 44453 but I still the same error Are you using some index file that is specifying a discontinuous water group? Have you properly re-created your genion input .tpr file from this new topology? -Justin 01 Nisan 2011 15:11 tarihinde Mark Abraham

Re: [gmx-users] The solvent group Water is not continuous

Is it a problem with an index file? is 'Water' an index group, and if so, is is contiguous. Erik ahmet yıldırım skrev 2011-04-01 14.15: I tried SOL 44453 but I still the same error 01 Nisan 2011 15:11 tarihinde Mark Abraham > yazdı: On 1/04/2011 11:03 PM,

Re: [gmx-users] The solvent group Water is not continuous

I tried SOL 44453 but I still the same error 01 Nisan 2011 15:11 tarihinde Mark Abraham yazdı: > On 1/04/2011 11:03 PM, ahmet yıldırım wrote: > > Dear Dr. Mark, > > I did you said but I have the same error. please look at attached file > > topol.top: > > [ molecules ] > ; Compound#mols

Re: [gmx-users] The solvent group Water is not continuous

On 1/04/2011 11:03 PM, ahmet yıldırım wrote: Dear Dr. Mark, I did you said but I have the same error. please look at attached file topol.top: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL 44125 TRS

Re: [gmx-users] The solvent group Water is not continuous

Dear Dr. Mark, I did you said but I have the same error. please look at attached file topol.top: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL 44125 TRS1 EDO1 01 Nis

Re: [gmx-users] The solvent group Water is not continuous

On 1/04/2011 10:26 PM, ahmet yıldırım wrote: Dear Justin, I have Fatal Errror:The solvent group Water is not continuous. I look at gmx-users mailing list search. I also have the same problem. You said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html) It is exactly what I

Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: Dear Justin, I have Fatal Errror:The solvent group Water is not continuous. I look at gmx-users mailing list search. I also have the same problem. You said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html) It is exactly what I said; you've proven

[gmx-users] The solvent group Water is not continuous

Dear Justin, I have Fatal Errror:The solvent group Water is not continuous. I look at gmx-users mailing list search. I also have the same problem. You said:( http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html) It is exactly what I said; you've proven it. You have solvent, ligan