[gmx-users] Problem building a polymer using pdb2gmx ....

Alberto Sergio Garay sgaray at fbcb.unl.edu.ar
Thu Sep 1 15:05:13 CEST 2011

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
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
Start terminus TQL-1: None
Select end terminus type for TEQ-34
0: COO-
2: None
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...

Any help will be appreciated...


Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221

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