Re: [AMBER] atom numbers

From: Vikas Sharma <vs_vikassharma.yahoo.co.in>
Date: Tue, 21 Apr 2009 16:33:12 +0100

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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com
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Received on Wed May 20 2009 - 12:07:28 PDT
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