Use a text editor like vi to view the prep file.
On Mar 3, 2018 9:40 AM, "Rana Rehan Khalid" <rrkhalid.umich.edu> wrote:
> can you please guide me how I can match my .pdb file with .prep. I can
> track the pdb with structure but how we track the .prep. Thanks
>
> On Sat, Mar 3, 2018 at 7:27 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > this likely means that the names of the atoms in your input pdb do not
> > match the names of the atoms in the input prep file. These need to match.
> >
> > On Sat, Mar 3, 2018 at 9:23 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
> > wrote:
> >
> > > Dear Amber users
> > >
> > > Kindly guide how I prepared the crd and prmtop files for protein system
> > > which have two Mg +2 ions nonbonded interaction with ASP and GTP . I
> > > download the GTP .prep file and frcmod file and follow these steps.
> > >
> > > source leaprc.protein.ff14SB
> > > source leaprc.water.tip3p
> > >
> > > addAtomTypes{
> > > > { "O3" "O" "sp2" }
> > > > }
> > > > loadamberparams frcmod.phos
> > > Loading parameters: ./frcmod.phos
> > > Reading force field modification type file (frcmod)
> > > Reading title:
> > > # Modifications to the AMBER94 force field for polyphosphates
> > > > loadamberprep GTP.prep
> > > Loading Prep file: ./GTP.prep
> > > Loaded UNIT: GTP
> > > > mol = loadpdb dimer-GTP.pdb
> > > Loading PDB file: ./dimer-GTP.pdb
> > > Enter zPdbReadScan from call depth 0.
> > > Exit zPdbReadScan from call depth 0.
> > > Matching PDB residue names to LEaP variables.
> > > Mapped residue VAL, term: Terminal/beginning, seq. number: 0 to: NVAL.
> > > (Residue 1: VAL, Nonterminal, was not found in name map.)
> > >
> > > mol = loadpdb dimer-GTP.pdb
> > > Loading PDB file: ./dimer-GTP.pdb
> > > Created a new atom named: HO3' within residue: .R<GTP 396>
> > > Created a new atom named: HO2' within residue: .R<GTP 396>
> > > Created a new atom named: HN22 within residue: .R<GTP 396>
> > > Created a new atom named: HN21 within residue: .R<GTP 396>
> > > Created a new atom named: HN1 within residue: .R<GTP 396>
> > > Created a new atom named: H2' within residue: .R<GTP 396>
> > > One sided connection. Residue: TP3 missing connect0 atom.
> > > total atoms in file: 6170
> > > Leap added 12 missing atoms according to residue templates:
> > > 12 H / lone pairs
> > > The file contained 6 atoms not in residue templates
> > > these all are the hydrogen of pentose sugar and Guanine. Kindly guide
> > how I
> > > resolve it thanks
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Received on Sat Mar 03 2018 - 07:00:02 PST
