On Wed, 2014-04-02 at 10:57 +0100, Vijay Manickam Achari wrote:
> I am trying to a load bilayer which contains molecules like lipid,
> water, and four tryptophan molecules with varying chains in xleap. I
> have prepared prepin files for the lipid and tryptophan molecules.
>
>
>
> source leaprc.ff12SB
> source leaprc.GLYCAM_06j_12SB
>
> loadamberprep lipid1.prepin
> loadamberprep Tryptofan1.prepin
> loadamberprep Tryptofan2.prepin
> loadamberprep Tryptofan3.prepin
> loadamberprep Tryptofan4.prepin
>
> sys = loadpdb bilayer.pdb
>
>
> I get message as below:
>
> vijay.glycosim:~/Simulation-Folder-Feb2013/other-systems/project-Osama/03-model-bilayers/1-preparation-system/MODEL-both/amber-format-forcefield$ xleap -f Vjnew-Octyl-TRP-Osama.xleap
> >-I: Adding /usr/local/apps/amber12/dat/leap/prep to search path.
> >-I: Adding /usr/local/apps/amber12/dat/leap/lib to search path.
> >-I: Adding /usr/local/apps/amber12/dat/leap/parm to search path.
> >-I: Adding /usr/local/apps/amber12/dat/leap/cmd to search path.
> >-f: Source Vjnew-Octyl-TRP-Osama.xleap.
> >
> >>
> >Welcome to LEaP!
> >(no leaprc in search path)
> >Sourcing: ./Vjnew-Octyl-TRP-Osama.xleap
> >----- Source: /usr/local/apps/amber12/dat/leap/cmd/leaprc.ff12SB
> >----- Source of /usr/local/apps/amber12/dat/leap/cmd/leaprc.ff12SB done
> >Log file: ./leap.log
> >Loading parameters: /usr/local/apps/amber12/dat/leap/parm/parm10.dat
> >Reading title:
> >PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> >Loading parameters: /usr/local/apps/amber12/dat/leap/parm/frcmod.ff12SB
> >Reading force field modification type file (frcmod)
> >Reading title:
> >ff12SB protein backbone and sidechain parameters
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/amino12.lib
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/aminoct12.lib
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/aminont12.lib
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/nucleic12.lib
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/ions08.lib
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/solvents.lib
> >----- Source: ./leaprc.GLYCAM_06j_12SB
> >----- Source of ./leaprc.GLYCAM_06j_12SB done
> >Loading parameters: ./GLYCAM_06j.dat
> >Reading title:
> >GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
> >Loading Prep file: ./GLYCAM_06j.prep
> >Loading library: ./GLYCAM_amino_06j_12SB.lib
> >Loading library: ./GLYCAM_aminoct_06j_12SB.lib
> >Loading library: ./GLYCAM_aminont_06j_12SB.lib
> >Substituting map 0HYP -> NHYP for 0HYP -> NHYP
> >Substituting map 1HYP -> CHYP for 1HYP -> CHYP
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/solvents.lib
> >Loading library: /usr/local/apps/amber12/dat/leap/lib/ions08.lib
> >Loading parameters: /usr/local/apps/amber12/dat/leap/parm/frcmod.ionsjc_tip3p
> >Reading force field modification type file (frcmod)
> >Reading title:
> >Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
> >Loading Prep file: ./lipid1.prepin
> >Loading Prep file: ./Tryptofan1.prepin
> >Loading Prep file: ./Tryptofan2.prepin
> >Loading Prep file: ./Tryptofan3.prepin
> >Loading Prep file: ./Tryptofan4.prepin
> >Loading PDB file: ./bilayer.pdb
> > (starting new molecule for chain J)
> >Warning: name change in pdb file residue 1 ;
> > this residue is split into TR0 and TR1.
> > (starting new molecule for chain I)
> >Warning: name change in pdb file residue 1 ;
> > this residue is split into TR1 and TR4.
> > (starting new molecule for chain H)
> >Warning: name change in pdb file residue 1 ;
> > this residue is split into TR4 and TR8.
> > (starting new molecule for chain G)
> >3 residues had naming warnings.
> > There are split residues;
> > residue sequence numbers will not correspond to those in the pdb.
> >-- residue 775: duplicate [ CA2] atoms (total 2)
> >-- residue 775: duplicate [ CA4] atoms (total 2)
[snip]
> >-- residue 778: duplicate [ OS8] atoms (total 2)
> >
> >>
> > Warning: Atom names in each residue should be unique.
> > (Same-name atoms are handled by using the first
> > occurrence and by ignoring the rest.
> > Frequently duplicate atom names stem from alternate
> > conformations in the PDB file.)
> >
> >>
> > total atoms in file: 11616
> >>
>
> I find no problem if I load each tryptophan in xleap. In fact I have
> changed all the "atom names" for each tryptophan. I also dont
> understand the lines highlighted in "blue" in the above output.
I see no blue lines. In general I would also discourage the use of HTML
markup and/or colors in email, since not all email clients support such
things. Plain text (with links to pastebin if necessary) is best.
>
> What I want is a topology file for my system.
>
> Is there any command to do this? How can combine and get a single
> topology and inpcrd file?
All I see here are warnings. If "saveAmberParm" failed, you didn't show
any error messages...
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 02 2014 - 05:00:08 PDT
