[gmx-users] pdb2gmx error
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 19 12:48:15 CEST 2012
Bishwajit Das wrote:
> Hi, i attached my pdb file,please check it... fixed.pdb is after fixing
> it into what if server and actin.pdb is original pdb file.The exact
> error is
>
The coordinate file is not in an order that Gromacs can work with. It is
arranged such that various groups of atoms are continuous rather than residues.
pdb2gmx will be unable to work with this file unless you re-order it so that
the residues are sequential.
-Justin
> Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
>
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
> Reading fixed.pdb...
> Read 'DUMMY', 2878 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> There are 2 chains and 0 blocks of water and 73 residues with 2878 atoms
>
> chain #res #atoms
> 1 'A' 2659 2867
> 2 'A' 1 11
>
>
> WARNING: there were 0 atoms with zero occupancy and 8 atoms with
> occupancy unequal to one (out of 2878 atoms). Check your pdb file.
>
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (amber99sb-ildn)
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
> Residue 93
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
> Residue 109
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
> Residue 125
> Sorting it all out...
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.6#
> Processing chain 1 'A' (2867 atoms, 2659 residues)
> There are 549 donors and 549 acceptors
> There are 773 hydrogen bonds
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/hizzie.c, line: 270
>
> Fatal error:
> Incomplete ring in HIS40
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> On Tue, Apr 10, 2012 at 1:35 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Bishwajit Das wrote:
>
> when i try to pdb2gmx -f *.pdb -o *_processed.gro -water spce
> command in my pdb file then i select AMBER99SB-ILDN force field
> (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) this force
> field but a error massage came.
> the massage is following:
>
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Identified residue GLU6 as a starting terminus.
> Identified residue GLU6 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus GLU-6: NH3+
> End terminus GLU-6: COO-
> Checking for duplicate atoms....
>
> ------------------------------__-------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file:
> /build/buildd/gromacs-4.5.4/__src/kernel/pgutil.c, line: 88
>
> Fatal error:
> Atom CG not found in residue seq.nr <http://seq.nr>
> <http://seq.nr>. 1 while adding atom
>
>
> For more information and tips for troubleshooting, please check
> the GROMACS
> website at http://www.gromacs.org/__Documentation/Errors
> <http://www.gromacs.org/Documentation/Errors>
> -------
> then i repair my protein with what if server as instruction
> given in gromacs documentation...then i again run the above
> process but still showing me a error massage.The massage was His
> 450 chain is not complete.How i overcome this problem..please
> give me a suggestion.
>
>
> The exact error message, copied and pasted from your terminal along
> with any other relevant output, would be useful. As it stands, the
> output you posted suggests that you have a single amino acid (since
> Glu-6 is both the start and end residue), but this is clearly not
> the case with the error at hand if something is wrong with His-450.
>
> No matter the case, the general solution is that the atom naming
> must match that of the .rtp entry for the residue being processed.
> If this is not true, either you are missing atoms or have a naming
> mismatch. If the error arises due to a hydrogen atom, either use
> -ignh to ignore H atoms in the input and rebuild them, or fix the
> naming mismatch.
>
> If you need further help, we need complete information.
>
> -Justin
>
> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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> --
> *
> BISHWAJIT DAS*//
> KOLKATA
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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