(unknown charset) [AMBER] Error in Simulation of MN2+ containing complex

From: (unknown charset) 杨川 <junaid.hust.edu.cn>
Date: Mon, 12 Jan 2015 16:19:32 +0800 (GMT+08:00)

Dear Amber users
I have a complex that contain a ligand and MN2+ ions . I use Amber14 for simulation. I downloaded the parameters for MN2+ from http://www.pharmacy.manchester.ac.uk/bryce/amber/. I use tleap to make topology for complex. but when i load the complex into the tleap ( i also checked the xleap version) it gives the following error and automatically quit the tleap. Any kind of help will be appriciated.

> com = loadpdb complex.pdb
Loading PDB file: ./complex.pdb
 (starting new molecule for chain )
-- residue 488: duplicate [ C] atoms (total 16)
-- residue 488: duplicate [ F] atoms (total 2)
-- residue 488: duplicate [ H] atoms (total 8)
-- residue 488: duplicate [ H1] atoms (total 2)
-- residue 488: duplicate [ H2] atoms (total 2)
-- residue 488: duplicate [ N] atoms (total 4)
-- residue 488: duplicate [ O] atoms (total 4)

   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.)

Created a new atom named: HD1 within residue: .R<HIE 293>
Created a new atom named: HE2 within residue: .R<GLU 318>
Created a new atom named: HD1 within residue: .R<HIE 320>
Created a new atom named: HD1 within residue: .R<HIE 335>
Created a new atom named: HD1 within residue: .R<HIE 341>
Created a new atom named: HD1 within residue: .R<HIE 392>
Created a new atom named: HD1 within residue: .R<HIE 398>
Created a new atom named: HC within residue: .R<CASN 486>
  Added missing heavy atom: .R<CASN 486>.A<OXT 15>
Bond: Maximum coordination exceeded on .R<LIG 488>.A<H1 28>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<LIG 488>.A<C 3> .R<LIG 488>.A<H1 28>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 445
!FATAL: Message: bondAtomProblem found
!
!ABORTING.

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Received on Mon Jan 12 2015 - 00:30:02 PST
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