Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

On 4/1/16 4:31 AM, bio hpc wrote: Did anybody of you wrote such script or can that be found in some repository? The specifics depend on the input file itself, and different programs write different names (an unfortunate truth that not everyone sticks to IUPAC/IUPAB nomenclature), and

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Did anybody of you wrote such script or can that be found in some repository? > El 31/3/2016, a las 13:04, Justin Lemkul escribió: > > > > On 3/31/16 6:55 AM, bio hpc wrote: >> Thanks. >> Apart from this, is is there some script that keeps my original hydrogens >> from

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

On 3/31/16 6:55 AM, bio hpc wrote: Thanks. Apart from this, is is there some script that keeps my original hydrogens from Maestro? Rename with sed according to what the force field expects. -Justin El 30/3/2016, a las 19:43, Tsjerk Wassenaar escribió: Hey :) -ignh

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Thanks. Apart from this, is is there some script that keeps my original hydrogens from Maestro? > El 30/3/2016, a las 19:43, Tsjerk Wassenaar escribió: > > Hey :) > > -ignh does ignore the hydrogens in the input file. It builds those > hydrogens that are specified in the

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hey :) -ignh does ignore the hydrogens in the input file. It builds those hydrogens that are specified in the force field. For histidines, the protonation state is determined from the possible hydrogen-bonded network, but it is possible to assign specific states interactively, using the option

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

I think using -ignh does not "remove" hydrogens. Hence, you can use it. Sent from my iPhone > On 30-Mar-2016, at 6:04 pm, rajendra kumar wrote: > > Hi, > > As suggested above, use -ignh to ignore hydrogen atoms. To use a specific > Histidine, you may change residue name HIS

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, As suggested above, use -ignh to ignore hydrogen atoms. To use a specific Histidine, you may change residue name HIS to HIP(Amber)/HSP(Charmm)/HISH( ​OPLS​ ) or HID(Amber)/HSD(Charmm)/HISD( ​OPLS​ ) or HIE(Amber)/HSE(Charmm)/HISE( ​OPLS​ ) either in PDB file or interactively through pdb2gmx

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, use -ignh flag in pdb2gmx, or you can use of "swiss pdbviewer" software to correct your pdb. On 3/30/16, bio hpc wrote: > Hi, > > we have created some protein pdb files with Maestro. When we try to un an MD > simulation with gromacs, we get errors like: > >>> Atom HD11

[gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, we have created some protein pdb files with Maestro. When we try to un an MD simulation with gromacs, we get errors like: >> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 atoms I tried to find a solution and it seems that internal gromacs dictionary for hydrogens is