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 <jalem...@vt.edu
<mailto:jalem...@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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