[gmx-users] renumbering residue numbers for version 4.0.2

[Nash, Anthony]

I figured it might of been something like that so I took out the second protein but I was still getting the same error message. Really odd.

I can give examples of the numbering, if that helps:

Topology order:
helixA          1
helixB          1
POPC            395
SOL         23765
CL              10

Gro file:
All atoms according to the topology file atoms numbered 1 to n. Residue numbers are 1 to k. In order of residue number helixA is 1 to 33 (of which I have made to reflect in the helixA.itp file), and 34 to 67 for helixB (as reflected in helixB.itp)

Start of helixA.itp
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue 1 ARG rtp ARG  q +1.0
     1         NL    1    ARG      N      1      -0.66    14.0067   ; qtot -0.66

Start  of helixB.itp
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue 34 ARG rtp ARG  q +1.0
     1         NL    34    ARG      N      1      -0.66    14.0067   ; qtot -0.66


I'm thinking of taking everything out of helixB.itp and putting it in helixA.itp, to make something like dimer.itp. But then that would involve making massive changes to the atom ids. 


Thanks
Anthony


________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
Sent: 29 March 2013 22:20
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] renumbering residue numbers for version 4.0.2

Looks like something is having trouble dealing with the second protein
segment. I would not expect the .itp residue numbering to be significant,
except that it changes between residues. Maybe the .gro and .itp residue
numbering had to match, back in that prehistoric era... Without seeing what
numbers things have, it's hard to say anything useful.

Mark

On Fri, Mar 29, 2013 at 6:26 PM, Nash, Anthony
<Anthony.Nash at warwick.ac.uk>wrote:

> Thanks for that, I've renumbered the residues in the .gro file, and even
> so far as in the respective protein .itp files. However, grompp is still
> throwing out the same error. Not sure where it is holding onto the number
> 652 (which is the start amino acid index of my protein) as I have reset the
> residue numbers to begin from 1.
>
> Residue numbers in the .top are not numbered consecutively from 1 (rather,
> resnumber = 652 and resnr_diff = -1)
>
> My top file is:
>
> #include "forcefield_popc.itp"
> #include "mut_helixA_renumber.itp"
> #include "mut_helixB_renumber.itp"
>
> #include "popc.itp"
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> #include "ions.itp"
>
> [ system ]
> Motif A oncogene in water
>
> [ molecules ]
> helixA          1
> helixB          1
> POPC            395
> SOL         23765
> CL              10
>
> The grompp command is:
> ~/gromacs-localpressure/bin/grompp_d -c starting_config.gro -n lateral.ndx
> -p ../../mut_system_renumber.top -o local_pressure -f local_pressure.mdp
>
> Any thoughts?
> Many thanks
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Mark Abraham [mark.j.abraham at gmail.com]
> Sent: 29 March 2013 14:17
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] renumbering residue numbers for version 4.0.2
>
> On Fri, Mar 29, 2013 at 2:10 PM, Nash, Anthony
> <Anthony.Nash at warwick.ac.uk>wrote:
>
> > Apologies if this has been covered once before, I've had a hearty search
> > and I've yet to find anything.
> >
> > I have just installed a modified verison of Gromacs 4.0.2 which calculate
> > lateral pressure. However, when I run grommp I get:
> >
> > Residue numbers in the .top are not numbered consecutively from 1
> (rather,
> > resnumber = 652 and resnr_diff = -1)
> >
> > Yet, running grompp on the same files with version 4.5.1 everything is
> > perfectly fine. I am guessing somewhere in between the two versions
> > something was changed.
> >
> > So, does this sound about right? Does the order of residue numbers no
> > longer mater with the latest versions of grompp? And ultimately, does
> > anyone know how I can go through a .gro file and renumber every residue
> > (short of writing a perl script)?
> >
>
> Use genconf -renumber from probably any version (and curse whoever thought
> that was a good place to put it :-))
>
> Mark
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