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

[Justin A. Lemkul]

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

========================================