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

[Alberto Sergio Garay]

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...

Any help will be appreciated...

Sergio

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