[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Alan]

I am using gmx 4.5 d748b.

Thanks Berk, it seems to be working ... for DNA.

But this one is broken (and it was working before): HHH is tripetide
Hie-Hie-Hie.

pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none

[snip]
Identified residue HIE1 as a starting terminus.
Identified residue HIE3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b
Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line:
916

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. Edit a .n.tdb and/or
.c.tdb file.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Alan

On 24 August 2010 15:30, Berk Hess <gmx3 at hotmail.com> wrote:

>  Hi,
>
> I fixed it.
> Thanks for the fast test and the complete instructions,
>
> Berk
>
> ------------------------------
> From: alanwilter at gmail.com
> Date: Tue, 24 Aug 2010 15:22:34 +0100
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
>
>
> Hi there, in special Berk.
>
> So pdb2gmx may be working with HIS and variants for oplsaa but now,
> something that was working before is failing:
>
> wget -c "http://www.pdbe.org/download/1BNA" -O 1BNA.pdb
> grep 'ATOM  ' 1BNA.pdb >| DNA.pdb
>
> cat << EOF >| SPE.mdp
> define = -DFLEXIBLE
> integrator               = md
> nsteps                   = 0
> dt                       = 0.001
> constraints              = none
> emtol                    = 10.0
> emstep                   = 0.01
> nstcomm                  = 1
> ns_type                  = simple
> nstlist                  = 0
> rlist                    = 0
> rcoulomb                 = 0
> rvdw                     = 0
> Tcoupl                   = no
> Pcoupl                   = no
> gen_vel                  = no
> nstxout                  = 1
> pbc                      = no
> nstlog = 1
> nstenergy = 1
> nstvout = 1
> nstfout = 1
> nstxtcout = 1
> comm_mode = ANGULAR
> continuation = yes
> EOF
>
> pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p
> DnaAmberSBGMX45
> [snip]
> 8 out of 8 lines of specbond.dat converted successfully
> [1]    42209 segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb
> -ff amber99sb -water none -p
>
> with 5e347 it worded fine, i.e, it opens files
>
> Opening force field file
> /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn
> Opening force field file
> /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn
> Opening force field file
> /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn
>
> and proceed.
>
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
>
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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