annalisa bordogna wrote:
Hi, Justin,
thank you for your reply.
I have just checked my .itp files.
I have 7 itp files:
- one is generated by doing genpr to define the restraints on the protein;
- six (two for each chain of my complex) are generated directly by
pdb2gmx (first step of my simulation).
The first itp file is ok: numbers are consecutive and starting from1.
The other six files have not consecutive numbers (I paste here the first
lines of one of these files):
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
Since they are automatically generated by pdb2gmx, how can I fix the
problem?
Let's go back to the original problem (which should not be related to the
position restraint files; they will not be numbered consecutively). The error
message states that the residue numbers are not numbered consecutively from 1.
Your problem is coming from residue numbering, not atomic numbering (apologies
for my typo in the last mail).
So you need to be examining the chain topologies and structure files to make
sure that the numbering matches up, and begins with 1.
-Justin
Thank you very much.
Annalisa
-----------------------------------------------------
Annalisa Bordogna
PhD. Student
DISAT - Università degli Studi di Milano Bicocca
Milano - Italy
-----------------------------------------------------
2009/4/6 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
annalisa bordogna wrote:
Hi everybody,
I am setting up an MD run on a peptide-protein complex with
gromacs. I have defined the box and solvated the system, but now
I'd like to equilibrate the solvent, so I tried with grompp, but
an error occurs:
Fatal error:
Residue numbers in the .top are not numbered consecutively from 1
I paste here my file .top:
; Include forcefield parameters
#include "ffG43a2.itp"
; Include chain topologies
#include "a.complex_A.itp"
#include "a.complex_B.itp"
#include "a.complex_C.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
Protein_C 1
SOL 28799
I have searched in the wiki and in the archives of the mailing
list, but I have found no hints on how I could fix it.
Does anybody know how can I manage to make grompp work?
The problem actually pertains to (at least) one of the chains you've
included. Numbering is inconsistent in that file. Check the .itp
files and make sure the atoms are numbered consecutively.
-Justin
Thank you in advance,
best regards,
Annalisa
-----------------------------------------------------
Annalisa Bordogna
PhD. Student
DISAT - Università degli Studi di Milano Bicocca
Milano - Italy
-----------------------------------------------------
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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