AMBER Archive (2009)

Subject: [AMBER] Parameter file not saved

From: Remya S R (amm07bi022_at_students.amrita.ac.in)
Date: Mon May 04 2009 - 07:03:08 CDT

Dear Amber users,
                        I got the following error when tried to run "tleap" during the simulation of DNA complexed with 2,5' bis(4-guanyl)furan. Please help me solve this!!!!!

The error is as follows
Loading PDB file: /home/student/remya/227D/complex_setup/227d_dna_BGF.pdb
Unknown residue: BGF number: 24 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: BGF sequence: 25
Created a new atom named: CA within residue: .R<BGF 25>
Created a new atom named: CB within residue: .R<BGF 25>
Created a new atom named: CB' within residue: .R<BGF 25>
Created a new atom named: CA' within residue: .R<BGF 25>
Created a new atom named: O1 within residue: .R<BGF 25>
Created a new atom named: C1 within residue: .R<BGF 25>
Created a new atom named: C2 within residue: .R<BGF 25>
Created a new atom named: C3 within residue: .R<BGF 25>
Created a new atom named: C4 within residue: .R<BGF 25>
Created a new atom named: C5 within residue: .R<BGF 25>
Created a new atom named: C6 within residue: .R<BGF 25>
Created a new atom named: C7 within residue: .R<BGF 25>
Created a new atom named: N1 within residue: .R<BGF 25>
Created a new atom named: N2 within residue: .R<BGF 25>
Created a new atom named: C1' within residue: .R<BGF 25>
Created a new atom named: C2' within residue: .R<BGF 25>
Created a new atom named: C3' within residue: .R<BGF 25>
Created a new atom named: C4' within residue: .R<BGF 25>
Created a new atom named: C5' within residue: .R<BGF 25>
Created a new atom named: C6' within residue: .R<BGF 25>
Created a new atom named: C7' within residue: .R<BGF 25>
Created a new atom named: N1' within residue: .R<BGF 25>
Created a new atom named: N2' within residue: .R<BGF 25>
Created a new atom named: HB within residue: .R<BGF 25>
Created a new atom named: HB' within residue: .R<BGF 25>
Created a new atom named: H2 within residue: .R<BGF 25>
Created a new atom named: H3 within residue: .R<BGF 25>
Created a new atom named: H5 within residue: .R<BGF 25>
Created a new atom named: H6 within residue: .R<BGF 25>
Created a new atom named: HN11 within residue: .R<BGF 25>
Created a new atom named: HN12 within residue: .R<BGF 25>
Created a new atom named: HN21 within residue: .R<BGF 25>
Created a new atom named: HN22 within residue: .R<BGF 25>
Created a new atom named: H2' within residue: .R<BGF 25>
Created a new atom named: H3' within residue: .R<BGF 25>
Created a new atom named: H5' within residue: .R<BGF 25>
Created a new atom named: H6' within residue: .R<BGF 25>
Created a new atom named: H1'1 within residue: .R<BGF 25>
Created a new atom named: H1'2 within residue: .R<BGF 25>
Created a new atom named: H2'1 within residue: .R<BGF 25>
Created a new atom named: H2'2 within residue: .R<BGF 25>
  total atoms in file: 801
  The file contained 41 atoms not in residue templates
Checking Unit.
WARNING: The unperturbed charge of the unit: -24.000000 is not zero.
FATAL: Atom .R<BGF 25>.A<CA 1> does not have a type.
FATAL: Atom .R<BGF 25>.A<CB 2> does not have a type.
FATAL: Atom .R<BGF 25>.A<CB' 3> does not have a type.
FATAL: Atom .R<BGF 25>.A<CA' 4> does not have a type.
FATAL: Atom .R<BGF 25>.A<O1 5> does not have a type.
FATAL: Atom .R<BGF 25>.A<C1 6> does not have a type.
FATAL: Atom .R<BGF 25>.A<C2 7> does not have a type.
FATAL: Atom .R<BGF 25>.A<C3 8> does not have a type.
FATAL: Atom .R<BGF 25>.A<C4 9> does not have a type.
FATAL: Atom .R<BGF 25>.A<C5 10> does not have a type.
FATAL: Atom .R<BGF 25>.A<C6 11> does not have a type.
FATAL: Atom .R<BGF 25>.A<C7 12> does not have a type.
FATAL: Atom .R<BGF 25>.A<N1 13> does not have a type.
FATAL: Atom .R<BGF 25>.A<N2 14> does not have a type.
FATAL: Atom .R<BGF 25>.A<C1' 15> does not have a type.
FATAL: Atom .R<BGF 25>.A<C2' 16> does not have a type.
FATAL: Atom .R<BGF 25>.A<C3' 17> does not have a type.
FATAL: Atom .R<BGF 25>.A<C4' 18> does not have a type.
FATAL: Atom .R<BGF 25>.A<C5' 19> does not have a type.
FATAL: Atom .R<BGF 25>.A<C6' 20> does not have a type.
FATAL: Atom .R<BGF 25>.A<C7' 21> does not have a type.
FATAL: Atom .R<BGF 25>.A<N1' 22> does not have a type.
FATAL: Atom .R<BGF 25>.A<N2' 23> does not have a type.
FATAL: Atom .R<BGF 25>.A<HB 24> does not have a type.
FATAL: Atom .R<BGF 25>.A<HB' 25> does not have a type.
FATAL: Atom .R<BGF 25>.A<H2 26> does not have a type.
FATAL: Atom .R<BGF 25>.A<H3 27> does not have a type.
FATAL: Atom .R<BGF 25>.A<H5 28> does not have a type.
FATAL: Atom .R<BGF 25>.A<H6 29> does not have a type.
FATAL: Atom .R<BGF 25>.A<HN11 30> does not have a type.
FATAL: Atom .R<BGF 25>.A<HN12 31> does not have a type.
FATAL: Atom .R<BGF 25>.A<HN21 32> does not have a type.
FATAL: Atom .R<BGF 25>.A<HN22 33> does not have a type.
FATAL: Atom .R<BGF 25>.A<H2' 34> does not have a type.
FATAL: Atom .R<BGF 25>.A<H3' 35> does not have a type.
FATAL: Atom .R<BGF 25>.A<H5' 36> does not have a type.
FATAL: Atom .R<BGF 25>.A<H6' 37> does not have a type.
FATAL: Atom .R<BGF 25>.A<H1'1 38> does not have a type.
FATAL: Atom .R<BGF 25>.A<H1'2 39> does not have a type.
FATAL: Atom .R<BGF 25>.A<H2'1 40> does not have a type.
FATAL: Atom .R<BGF 25>.A<H2'2 41> does not have a type.
Failed to generate parameters
Parameter file was not saved.
        Quit

The input file for tleap is as follows

source leaprc.ff03
source leaprc.gaff
mods=loadamberparams /home/student/remya/227D/complex_setup/BGF.frcmod
BGF=loadmol2 /home/student/remya/227D/complex_setup/BGF.mol2

complex=loadpdb /home/student/remya/227D/complex_setup/227d_dna_BGF.pdb

saveamberparm complex /home/student/remya/227D/complex_setup/227d_complex.prmtop /home/student/remya/227D/complex_setup/227d_complex.inpcrd

quit

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