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)
>-- residue 775: duplicate [ CA6] atoms (total 2)
>-- residue 775: duplicate [ CA8] atoms (total 2)
>-- residue 775: duplicate [ CA9] atoms (total 2)
>-- residue 775: duplicate [ CB1] atoms (total 2)
>-- residue 775: duplicate [ CB5] atoms (total 2)
>-- residue 775: duplicate [ CB6] atoms (total 2)
>-- residue 775: duplicate [ CB9] atoms (total 2)
>-- residue 775: duplicate [ CC5] atoms (total 2)
>-- residue 775: duplicate [ CC7] atoms (total 2)
>-- residue 775: duplicate [ HA1] atoms (total 2)
>-- residue 775: duplicate [ HA3] atoms (total 2)
>-- residue 775: duplicate [ HA5] atoms (total 2)
>-- residue 775: duplicate [ HA7] atoms (total 2)
>-- residue 775: duplicate [ HB2] atoms (total 2)
>-- residue 775: duplicate [ HB4] atoms (total 2)
>-- residue 775: duplicate [ HB7] atoms (total 2)
>-- residue 775: duplicate [ HB8] atoms (total 2)
>-- residue 775: duplicate [ HC1] atoms (total 2)
>-- residue 775: duplicate [ HC2] atoms (total 2)
>-- residue 775: duplicate [ HC3] atoms (total 2)
>-- residue 775: duplicate [ HC8] atoms (total 2)
>-- residue 775: duplicate [ NB3] atoms (total 2)
>-- residue 775: duplicate [ NC4] atoms (total 2)
>-- residue 775: duplicate [ OC6] atoms (total 2)
>-- residue 775: duplicate [ OC9] atoms (total 2)
>-- residue 776: duplicate [ CD2] atoms (total 2)
>-- residue 776: duplicate [ CD4] atoms (total 2)
>-- residue 776: duplicate [ CD6] atoms (total 2)
>-- residue 776: duplicate [ CD8] atoms (total 2)
>-- residue 776: duplicate [ CD9] atoms (total 2)
>-- residue 776: duplicate [ CE1] atoms (total 2)
>-- residue 776: duplicate [ CE5] atoms (total 2)
>-- residue 776: duplicate [ CE6] atoms (total 2)
>-- residue 776: duplicate [ CE9] atoms (total 2)
>-- residue 776: duplicate [ CF5] atoms (total 2)
>-- residue 776: duplicate [ CF7] atoms (total 2)
>-- residue 776: duplicate [ CG3] atoms (total 2)
>-- residue 776: duplicate [ HD1] atoms (total 2)
>-- residue 776: duplicate [ HD3] atoms (total 2)
>-- residue 776: duplicate [ HD5] atoms (total 2)
>-- residue 776: duplicate [ HD7] atoms (total 2)
>-- residue 776: duplicate [ HE2] atoms (total 2)
>-- residue 776: duplicate [ HE4] atoms (total 2)
>-- residue 776: duplicate [ HE7] atoms (total 2)
>-- residue 776: duplicate [ HE8] atoms (total 2)
>-- residue 776: duplicate [ HF1] atoms (total 2)
>-- residue 776: duplicate [ HF2] atoms (total 2)
>-- residue 776: duplicate [ HF3] atoms (total 2)
>-- residue 776: duplicate [ HF9] atoms (total 2)
>-- residue 776: duplicate [ HG1] atoms (total 2)
>-- residue 776: duplicate [ HG2] atoms (total 2)
>-- residue 776: duplicate [ NE3] atoms (total 2)
>-- residue 776: duplicate [ NF4] atoms (total 2)
>-- residue 776: duplicate [ OF6] atoms (total 2)
>-- residue 776: duplicate [ OF8] atoms (total 2)
>-- residue 777: duplicate [ CI2] atoms (total 2)
>-- residue 777: duplicate [ CI4] atoms (total 2)
>-- residue 777: duplicate [ CI6] atoms (total 2)
>-- residue 777: duplicate [ CI8] atoms (total 2)
>-- residue 777: duplicate [ CI9] atoms (total 2)
>-- residue 777: duplicate [ CJ1] atoms (total 2)
>-- residue 777: duplicate [ CJ5] atoms (total 2)
>-- residue 777: duplicate [ CJ6] atoms (total 2)
>-- residue 777: duplicate [ CJ9] atoms (total 2)
>-- residue 777: duplicate [ CM5] atoms (total 2)
>-- residue 777: duplicate [ CM7] atoms (total 2)
>-- residue 777: duplicate [ CN2] atoms (total 2)
>-- residue 777: duplicate [ CN5] atoms (total 2)
>-- residue 777: duplicate [ CN8] atoms (total 2)
>-- residue 777: duplicate [ CP3] atoms (total 2)
>-- residue 777: duplicate [ HI1] atoms (total 2)
>-- residue 777: duplicate [ HI3] atoms (total 2)
>-- residue 777: duplicate [ HI5] atoms (total 2)
>-- residue 777: duplicate [ HI7] atoms (total 2)
>-- residue 777: duplicate [ HJ2] atoms (total 2)
>-- residue 777: duplicate [ HJ4] atoms (total 2)
>-- residue 777: duplicate [ HJ7] atoms (total 2)
>-- residue 777: duplicate [ HJ8] atoms (total 2)
>-- residue 777: duplicate [ HM1] atoms (total 2)
>-- residue 777: duplicate [ HM2] atoms (total 2)
>-- residue 777: duplicate [ HM3] atoms (total 2)
>-- residue 777: duplicate [ HM9] atoms (total 2)
>-- residue 777: duplicate [ HN1] atoms (total 2)
>-- residue 777: duplicate [ HN3] atoms (total 2)
>-- residue 777: duplicate [ HN4] atoms (total 2)
>-- residue 777: duplicate [ HN6] atoms (total 2)
>-- residue 777: duplicate [ HN7] atoms (total 2)
>-- residue 777: duplicate [ HN9] atoms (total 2)
>-- residue 777: duplicate [ HP1] atoms (total 2)
>-- residue 777: duplicate [ HP2] atoms (total 2)
>-- residue 777: duplicate [ NJ3] atoms (total 2)
>-- residue 777: duplicate [ NM4] atoms (total 2)
>-- residue 777: duplicate [ OM6] atoms (total 2)
>-- residue 777: duplicate [ OM8] atoms (total 2)
>-- residue 778: duplicate [ CQ2] atoms (total 2)
>-- residue 778: duplicate [ CQ4] atoms (total 2)
>-- residue 778: duplicate [ CQ6] atoms (total 2)
>-- residue 778: duplicate [ CQ9] atoms (total 2)
>-- residue 778: duplicate [ CR1] atoms (total 2)
>-- residue 778: duplicate [ CR5] atoms (total 2)
>-- residue 778: duplicate [ CR6] atoms (total 2)
>-- residue 778: duplicate [ CR8] atoms (total 2)
>-- residue 778: duplicate [ CR9] atoms (total 2)
>-- residue 778: duplicate [ CS5] atoms (total 2)
>-- residue 778: duplicate [ CS7] atoms (total 2)
>-- residue 778: duplicate [ CU2] atoms (total 2)
>-- residue 778: duplicate [ CU5] atoms (total 2)
>-- residue 778: duplicate [ CU8] atoms (total 2)
>-- residue 778: duplicate [ CV2] atoms (total 2)
>-- residue 778: duplicate [ CV5] atoms (total 2)
>-- residue 778: duplicate [ CV8] atoms (total 2)
>-- residue 778: duplicate [ CX2] atoms (total 2)
>-- residue 778: duplicate [ CX6] atoms (total 2)
>-- residue 778: duplicate [ HQ1] atoms (total 2)
>-- residue 778: duplicate [ HQ3] atoms (total 2)
>-- residue 778: duplicate [ HQ5] atoms (total 2)
>-- residue 778: duplicate [ HQ7] atoms (total 2)
>-- residue 778: duplicate [ HR2] atoms (total 2)
>-- residue 778: duplicate [ HR4] atoms (total 2)
>-- residue 778: duplicate [ HR7] atoms (total 2)
>-- residue 778: duplicate [ HR8] atoms (total 2)
>-- residue 778: duplicate [ HS1] atoms (total 2)
>-- residue 778: duplicate [ HS2] atoms (total 2)
>-- residue 778: duplicate [ HS3] atoms (total 2)
>-- residue 778: duplicate [ HS9] atoms (total 2)
>-- residue 778: duplicate [ HU1] atoms (total 2)
>-- residue 778: duplicate [ HU3] atoms (total 2)
>-- residue 778: duplicate [ HU4] atoms (total 2)
>-- residue 778: duplicate [ HU6] atoms (total 2)
>-- residue 778: duplicate [ HU7] atoms (total 2)
>-- residue 778: duplicate [ HU9] atoms (total 2)
>-- residue 778: duplicate [ HV1] atoms (total 2)
>-- residue 778: duplicate [ HV3] atoms (total 2)
>-- residue 778: duplicate [ HV4] atoms (total 2)
>-- residue 778: duplicate [ HV6] atoms (total 2)
>-- residue 778: duplicate [ HV7] atoms (total 2)
>-- residue 778: duplicate [ HV9] atoms (total 2)
>-- residue 778: duplicate [ HX1] atoms (total 2)
>-- residue 778: duplicate [ HX3] atoms (total 2)
>-- residue 778: duplicate [ HX4] atoms (total 2)
>-- residue 778: duplicate [ HX5] atoms (total 2)
>-- residue 778: duplicate [ NR3] atoms (total 2)
>-- residue 778: duplicate [ NS4] atoms (total 2)
>-- residue 778: duplicate [ OS6] atoms (total 2)
>-- 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.
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?
Any help is much appreciated.
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Wed Apr 02 2014 - 03:00:03 PDT
