Thank you. I will try accordingly.
On Sat, Jun 21, 2014 at 7:04 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Update your AmberTools. Before uploading any receptor prepare it using MMV
> or Glide. To solve this open your rec.pdb with MMV, which will
> automatically correct your receptor. After saving it in .pdb format; open
> it again with Chimera and delete all hydrogens and save it as rec.pdb
> format.
>
> try this tleap file. I presume you are running a typical ligand and
> receptor complex. Update AmberTools i
>
> source leaprc.ff99SB
> source leaprc.gaff
> LIG = loadmol2 LIG.mol2
> loadamberparams LIG.frcmod
> check LIG
> receptor = loadPDB rec.pdb
> complex = combine {receptor LIG}
> set default PBRadii mbondi2
> saveAmberParm LIG LIG.top LIG.crd
> receptor = loadPDB rec.pdb
> saveAmberParm receptor rec.top rec.crd
> saveAmberParm complex com.top com.crd
> savepdb complex complex_gas.pdb
> charge complex
> addIons2 complex Na+ 0
> solvateBox complex TIP3PBOX 8.0
> saveAmberParm complex com_solvated.top com_solvated.crd
> savepdb complex com_solvated.pdb
> quit
>
> Best,
> SB
>
>
> On Sat, Jun 21, 2014 at 2:56 PM, Shomesankar Bhunia <
> rightclickatrighttime.gmail.com> wrote:
>
> > Dear all,
> > I am having a problem while setting a system for MD simulation in amber.
> > I am having a ligand bound at the interface of two protein structures. I
> am
> > using reduce to trim the the hydrogens and applying tleap to add
> hydrogens.
> > I am getting segmentation fault while loading the protein ligand
> > complex.The command line is
> >
> > ./tleap -f leaprc.ff99SBildn
> > >source leaprc.gaff
> >
> > >loadamberparams lig_m.frcmod
> > Loading parameters: ./azixa_lig_m.frcmod
> > Reading force field modification type file (frcmod)
> > Reading title:
> > remark goes here
> >
> >
> > >loadoff lig_m.lib
> > Loading library: ./azixa_lig_m.lib
> >
> > >complex = loadpdb lig_prot_noh.pdb
> > Loading PDB file: ./azixa_lig_prot_noh.pdb
> > Added missing heavy atom: .R<CGLY 436>.A<OXT 8>
> > Added missing heavy atom: .R<CASP 853>.A<OXT 13>
> > Segmentation fault (core dumped)
> >
> >
> > The GLY 436 and ASP 853 are the terminal residues of the two protein
> > structures respectively. How to overcome the problem? Thanks in advance.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jun 21 2014 - 07:00:03 PDT
