[gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx

s... Fatal error: atom name O3PB not found in residue ATP 340 while generating exclusions How can I resolve this first not done by -missing command? Cheers, Una -- Una Bjarnadottir School of Biomolecular and Biomedical Science Conway Institute UCD Dublin 4, Ireland P

[gmx-users] Conjugate Gradient - Equations

Hi everyone, In the gromacs manual the equations regarding the conjugate gradient are not shown. Is there anybody that can help me find them or send them to me? Cheers, Una ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] RMSF and temperature factors

Dear users, I have been trying to find information about the equation, which is used in GROMACS to converts RMSF values to temperature factors. I know NAMD uses: B = (RMSF2 x 8π2)/3 and would like to know if the same is used in GROMACS. Cheers, Una begin:vcard fn:Una Bjarnadottir n:Bjarnadott

[gmx-users] partial charges, editconf -grasp

exact same error. Can anyone help me with this problem? Is there perhaps an easier way of getting the partial charges? Kind regards, Una -- Una Bjarnadottir School of Biomolecular and Biomedical Science Conway Institute UCD Dublin 4, Ireland Phone: +353 1 716 6874, Fax:

[gmx-users] Implicit Solvent Simulations

To the Gromacs user community, As of April 2007 it was not possible to do implicit solvent MDs with Gromacs (http://www.gromacs.org/pipermail/gmx-users/2007-April/026849.html). Has this changed since then? Kind regards, Una -- Una Bjarnadottir School of Biomolecular and Biomedical

[gmx-users] Re: Fatal error: Error: Too many iterations in routine JACOBI

you didn't run trjconv on the trajectory with certain the -pbc options. Cheers, Tsjerk On 5/29/07, Una Bjarnadottir <[EMAIL PROTECTED]> wrote: Dear users, I'm using g_covar to analyse my trajectories and saw here on the list that the one should use the average structure as t

[gmx-users] Fatal error: Error: Too many iterations in routine JACOBI

Dear users, I'm using g_covar to analyse my trajectories and saw here on the list that the one should use the average structure as the reference structre in the -s option in g_covar. I made my average structure with g_rmsf but when I ran g_covar g_covar -f md.trr -s xaver.pdb -ascii covar.da

[gmx-users] Re: Re: trjconv and missing chain identifier

example? Best regards, Una Una Bjarnadottir wrote: > Dear Users, > > I'm converting trajectory files into .pdb files and when there is only > the protein chain in them i.e. only the protein but not ligand or inhibitor > it does not set any chain identifier to the output .pdb f

[gmx-users] trjconv and missing chain identifier

A-B-C. I tryed whatif but it can't read the big overall file. The chain identifier is nessarry in some grafics programs so I really need this. Hope you can help, it will be hightly appreciated. Cheers, Una Una Bjarnadottir Conway Institute Department of Biochemistry Belfield Dublin 4 Ire

[gmx-users] Re: Re: GENION: Ions inside the protein (Viswanadham Sridhara & Tsjerk Wassenaar)

r the resulting .gro file using genconf, make a new index file and start running. On 10/10/06, Una Bjarnadottir <[EMAIL PROTECTED]> wrote: Dear users, In some of my simulations after neutralizing the systems with genion 2 of the ions were inside the active site cleft of the prot

[gmx-users] GENION: Ions inside the protein

r way to delete the solvent within the protein did I misunderstand that so those water molecules will not be replaced? Best regards, Una Bjarnadottir ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-

[gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

Una Bjarnadottir wrote: Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

[gmx-users] genion causing atom to be in multiple T-Coupling groups

ions. Please help because have not been able to fix the problem with related letters on the subject on the list. Best regards, Una Bjarnadottir .top before: ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound

[gmx-users] genion causing atom to be in multiple T-Coupling groups

e and took 3 sol molecules and added the 3 ions. _* *_Best regards for any help, Una Bjarnadottir _* .top before: *_; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_E 1 Protein_I

[gmx-users] missing atom in .rpb: fatal error in pdb2gmx

b2gmx complaining about this atom in the first place? Thanks in advance, replys are highly appreciated. Una Bjarnadottir ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un

[gmx-users] segmentation fault when using g_hbond

gards, Una Bjarnadottir ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't

[gmx-users] pdb2gmx atom not found

Una Bjarnadottir wrote: Dear users, I keep getting this error when starting runs; Opening library file aminoacids.dat --- Program pdb2gmx, VERSION 3.3 Source code file: add_par.c, line: 221 Fatal error: Atom NZ1 not found in rtp database in

[gmx-users] pdb2gmx atom not found

Dear users, I keep getting this error when starting runs; Opening library file aminoacids.dat --- Program pdb2gmx, VERSION 3.3 Source code file: add_par.c, line: 221 Fatal error: Atom NZ1 not found in rtp database in residue LYSH, it looks a b