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
