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.biomaps.rutgers.edu>
To: AMBER Mailing List <amber.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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Received on Wed May 20 2009 - 12:07:28 PDT