AMBER Archive (2009)

Subject: Re: [AMBER] atom numbers

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Tue Apr 21 2009 - 10:33:12 CDT

Hi Dr. david Case

I am working on MM PBSA..I am using xleap..
i did this:
       
        "source leaprc.ff03
        source leaprc.gaff
        com = loadpdb 'prot-ligand complex.pdb'

it gave the result as:

        residue 317:duplicate [c] atoms (total 2)
        residue 317:duplicate [o] atoms (total 4)
        warning: atom names in each residue should be unique. (same-name atom are             handled by using the first occut=rence and by ignoring the rest. Frequently                 duplicate         atom names stem from alternate conformations in the PDB file).
       
        Unknown residue: M_$ no:221 type:terminal/last
        ...relaxing & constraints to try for a database match - no luck
 
        Added mising heavy atom:R<C THR 316>.A<OXT 15>
 
        Creating a new unit for residue : M_4 sequence:317
        Created a new atom name:C in residue:.R<M_4 317>
        Created a new atom name:O in residue:.R<M_4 317>
        Created a new atom name:H2O in residue:.R<M_4 317>
        Created a new atom name:C4 in residue:.R<M_4 317>
        Created a new atom name:C3 in residue:.R<M_4 317>
        Created a new atom name:C2 in residue:.R<M_4 317>
        Created a new atom name:H1 in residue:.R<M_4 317>
        Created a new atom name:H2 in residue:.R<M_4 317>
        Created a new atom name:H21 in residue:.R<M_4 317>
        Created a new atom name:H3 in residue:.R<M_4 317>
        Created a new atom name:H4 in residue:.R<M_4 317>
        Created a new atom name:N6 in residue:.R<M_4 317>
        Created a new atom name:C7 in residue:.R<M_4 317>
        Created a new atom name:O8 in residue:.R<M_4 317>
        Created a new atom name:C10 in residue:.R<M_4 317>
        Created a new atom name:C11 in residue:.R<M_4 317>
        Created a new atom name:C12 in residue:.R<M_4 317>
        Created a new atom name:C13 in residue:.R<M_4 317>
        Created a new atom name:C14 in residue:.R<M_4 317>
        Created a new atom name:C15 in residue:.R<M_4 317>
        Created a new atom name:H9 in residue:.R<M_4 317>
        Created a new atom name:H8 in residue:.R<M_4 317>
        Created a new atom name:N16 in residue:.R<M_4 317>
        Created a new atom name:C28 in residue:.R<M_4 317>
        Created a new atom name:C21 in residue:.R<M_4 317>
        Created a new atom name:C22 in residue:.R<M_4 317>
        Created a new atom name:N23 in residue:.R<M_4 317>
        Created a new atom name:C24 in residue:.R<M_4 317>
        Created a new atom name:C25 in residue:.R<M_4 317>
        Created a new atom name:C26 in residue:.R<M_4 317>
        Created a new atom name:C 27in residue:.R<M_4 317>
        Created a new atom name:C 28 in residue:.R<M_4 317>
        Created a new atom name:N25 in residue:.R<M_4 317>
        Created a new atom name:C26 in residue:.R<M_4 317>
        Created a new atom name:N30 in residue:.R<M_4 317>
        Created a new atom name:H18 in residue:.R<M_4 317>
        Created a new atom name:H19 in residue:.R<M_4 317>
        Created a new atom name:N29 in residue:.R<M_4 317>
        Created a new atom name:H16 in residue:.R<M_4 317>
        Created a new atom name:H17 in residue:.R<M_4 317>
        Created a new atom name:H10 in residue:.R<M_4 317>
        Created a new atom name:H14 in residue:.R<M_4 317>
        Created a new atom name:H15 in residue:.R<M_4 317>
        Created a new atom name:C27 in residue:.R<M_4 317>
        Created a new atom name:H11 in residue:.R<M_4 317>
        Created a new atom name:H12 in residue:.R<M_4 317>
        Created a new atom name:H13 in residue:.R<M_4 317>
        Created a new atom name:CL31 in residue:.R<M_4 317>
        Created a new atom name:H7 in residue:.R<M_4 317>
        Created a new atom name:H6 in residue:.R<M_4 317>
        Created a new atom name:H5 in residue:.R<M_4 317>
        total atoms in file = 1889
        leap added 1877 missing atoms according to residue templates
        1 heavy
        1876 H/lone pairs
        file contained 47 atoms not in residue templates
 
M_4  is the ligand..
 
when i used antechamber - i ligand.mol2 -fi mol2 -o ligand.prepin -fo prepi -c bcc -s 2
then parmchk -i ligand.prepin -f prepi -o ligand.frcmod
then loadamberprep ligand.prepin
loadamberparams ligand.frcmod
then in xleap when i load the 'prot-ligand complex'
it quits leap and gives the following error
 
        fatal error......
        !fatal:In file[atom.c],line 444
        !fatal: meaasage: bondAtomProblem found
        !       
        !Aborting
i opened the ligand mol2 file and ligand-protein complex pdb file and found 2 carbons and 4 oxygens having no number...

help??????????

________________________________
From: David A. Case <case_at_biomaps.rutgers.edu>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Tuesday, 21 April, 2009 5:24:37 PM
Subject: Re: [AMBER] atom numbers

On Tue, Apr 21, 2009, Vikas Sharma wrote:
>
> when i try to load the protein-ligand complex PDB, it gives the warning
> that "atom numbers should be unique....."

Can you please quote (cut and paste) the *exact* error or warning
message, and how you obtained it?  From your message, it's not even
clear what program you are running.  Is this input you prepared, or is
it from one of the tutorials?

Is it possible you are seeing a message about atom *names*?

...dac

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