Alberto Sergio Garay wrote:
Hi All
I'm building a polymer (heterodimer) using pdb2gmx tool. I have included
in ffG53a6 the 4 building block I need (aminoacids.rtp in my own dir:
../my_ffG53a6..):
X ... A-B-A-B-A-B-A-B-A-B-A ... Y
X: starting CAP residue
A: a monomer
B: the other monomer
Y: terminal CAP residue
I have to mention that I've already done this successfully with a
gromacs version 4.0.5, but now I can't do it in gromacs 4.5.4...
I have also added the 4 new residues into the file: residuetype.dat
When I run the following line:
g_pdb2gmx -f pol35.pdb -p top -o pol35 -ff my_gromos53a6 -ter
It gives me:
Using the My_gromos53a6 force field in directory ./my_gromos53a6.ff
Opening force field file ./my_gromos53a6.ff/watermodels.dat
Select the Water Model:
1: SPC simple point charge, recommended
2: SPC/E extended simple point charge
3: None
1
Opening force field file ./my_gromos53a6.ff/aminoacids.r2b
Reading pol35.pdb...
Read 'Glycine aRginine prOline Methionine Alanine Cystine Serine', 729
atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 35 residues with 729 atoms
chain #res #atoms
1 ' ' 35 729
All occupancies are one
Opening force field file ./my_gromos53a6.ff/atomtypes.atp
Atomtype 1
Reading residue database... (my_gromos53a6)
Opening force field file ./my_gromos53a6.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 119
Sorting it all out...
Opening force field file ./my_gromos53a6.ff/aminoacids.hdb
Opening force field file ./my_gromos53a6.ff/aminoacids.n.tdb
Opening force field file ./my_gromos53a6.ff/aminoacids.c.tdb
Back Off! I just backed up top.top to ./#top.top.1#
Processing chain 1 (729 atoms, 35 residues)
There are 28 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue TQL1 as a starting terminus.
Warning: Residue VBR35 in chain has different type (Other) from starting
residue TQL1 (Protein).
Identified residue TEQ34 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for TQL-1
0: NH3+
1: NH2
2: None
2
Start terminus TQL-1: None
Select end terminus type for TEQ-34
0: COO-
1: COOH
2: None
2
End terminus TEQ-34: None
-------------------------------------------------------
Program g_pdb2gmx, VERSION 4.5.4
Source code file:
/builddir/build/BUILD/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1035
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I don't understand why pdb2gmx takes the 34th residue as the last
monomer when in fact it has 35... After the error I understood why
pdb2gmx complains about: ..a dangling bond...
But I do not know how to solve the problem ....I need that pdb2gmx uses
my last 35th monomer as the last one...
The reason was printed to the screen:
"Warning: Residue VBR35 in chain has different type (Other) from starting
residue TQL1 (Protein)."
Chains have to be all one type in order to be continuous. So, either all of
your buildings blocks have to be defined as Protein or all of them have to be
defined as Other.
-Justin
--
========================================
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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