[gmx-users] Dangling bond error using Amber force field.

Wang, Yang Yang.Wang10 at utdallas.edu
Fri Jun 1 17:18:35 CEST 2018 

Hi ,

I attached the PDB. It seems like cap ACE is listed in front of the main body of the chain but NME is separated from the chain and listed in the last part of the pbd file. And gromacs cannot tell that NME acrually belongs to each chain and thus separate all the NME to be a chain by itself. Right now I am moving the NME back to the tail part of each chain. I am not sure whether this is right way. Thanks a lot!



Best Regards,

Yang Wang



Ph.D. student

Department of Mechanical Engineering

University of Texas at Dallas

E-mail: yxw152130 at utdallas.edu<mailto:sxw141830 at utdallas.edu>


________________________________
From: Wang, Yang
Sent: Friday, June 1, 2018 10:13:01 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Dangling bond error using Amber force field.


Hi ,


I attached the PDB. It seems like cap ACE is listed in front of the main body of the chain but NME is separated from the chain and listed in the last part of the pbd file. And gromacs cannot tell that NME acrually belongs to each chain and thus separate all the NME to be a chain by itself. Right now I am moving the NME back to the tail part of each chain. I am not sure whether this is right way. Thanks a lot!


Best Regards,

Yang Wang



Ph.D. student

Department of Mechanical Engineering

University of Texas at Dallas

E-mail: yxw152130 at utdallas.edu<mailto:sxw141830 at utdallas.edu>


________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Friday, June 1, 2018 10:04:53 AM
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Dangling bond error using Amber force field.

Hi,

Chain 16 is clearly a problem (start and end residue is NME 8) but you'll
have to look at the contents of the pdb file to understand its contents.

Mark

On Fri, Jun 1, 2018, 16:33 Wang, Yang <Yang.Wang10 at utdallas.edu> wrote:

> Hi,
>
> I am dealing with a protein model using Gromacs. I got the PDB file from
> RCSB bank (PID: 2slk) and I modified the residue name according to the rtp
> file. Since the start terminal is ACE, I modified the end terminal from
> GLY/ALA to CGLY/CALA.  I ran it with pdb2gmx command but I still got the
> dangling bond error.  The error message showed that the error came from the
> last chain of NEM residues. I guess it is probably still the name issue for
> the NEM cap. I am wondering what residue name I should use for NEM.
> Thanks a lot!
>
> Command:
> login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water
> tip3p -ignh
>
> Error:
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Select the Force Field:
> From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
>  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> 1999-2012, 2003)
> ..........( Omit the other force fields)
>
> 1
>
> Using the Amber03 force field in directory
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff
>
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
> Reading 2slk.pdb...
> WARNING: all CONECT records are ignored
> Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> There are 16 chains and 0 blocks of water and 106 residues with 480 atoms
>
>   chain  #res #atoms
>   1 'A'     7     30
>   2 'B'     7     30
>   3 'C'     7     30
>   4 'D'     7     30
>   5 'E'     7     30
>   6 'F'     7     30
>   7 'G'     7     30
>   8 'H'     7     30
>   9 'I'     7     30
>   10 'J'     7     30
>   11 'K'     7     30
>   12 'L'     7     30
>   13 'M'     7     30
>   14 'N'     7     30
>   15 'O'     7     30
>   16 'A'     1     30
>
> All occupancies are one
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/atomtypes.atp
> Atomtype 68
> Reading residue database... (amber03)
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.rtp
> Residue 93
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.rtp
> Residue 109
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.rtp
> Residue 125
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.n.tdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.c.tdb
>
> ..........( Omit the chain 1-15)
>
>
> Processing chain 16 'A' (30 atoms, 1 residues)
> Identified residue NME8 as a starting terminus.
> Identified residue NME8 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program gmx pdb2gmx, VERSION 5.1.2
> Source code file:
> /admin/rpms/BUILD/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
> line: 1083
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends and the
> force field does not provide terminal entries or files. Fix your terminal
> residues so that they match the residue database (.rtp) entries, or provide
> terminal database entries (.tdb).
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
> Best Regards,
>
> Yang Wang
>
>
>
> Ph.D. student
>
> Department of Mechanical Engineering
>
> University of Texas at Dallas
>
> E-mail: yxw152130 at utdallas.edu<mailto:sxw141830 at utdallas.edu>
>
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