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 - 06:30:04 PST
