[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Thu Jul 10 11:44:28 CEST 2014
hello every one
i have been removed all the error of previous output but still i got one
new error
Fatal error:
[ file strong_posre.itp, line 3886 ]:
Atom index (3882) in position_restraints out of bounds (1-3881).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
i have been changed the position_restrints but no out put same error
please help
topol.top
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif
; Include ligand topology
#include "drag.itp"
; Include POPC chain topology
#include "popc.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
On Thu, Jul 10, 2014 at 10:46 AM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:
> hello every one
> ohk i havbben pasted UNK portion from old files because it is still
> missing in system.gro now after running minimization i got new error old
> problem has resolved
> :-) grompp (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -f minim.mdp Input grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c system_inflated.gro Input Structure file: gro g96 pdb tpr etc.
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
> -n index.ndx Input, Opt. Index file
> -p topol.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o confout.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -[no]version bool no Print version info and quit
> -nice int 0 Set the nicelevel
> -[no]v bool no Be loud and noisy
> -time real -1 Take frame at or first after this time.
> -[no]rmvsbds bool yes Remove constant bonded interactions with
> virtual
> sites
> -maxwarn int 2 Number of allowed warnings during input
> processing. Not for normal use and may generate
> unstable systems
> -[no]zero bool no Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum bool yes Renumber atomtypes and minimize number of
> atomtypes
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
> Generated 813 of the 2346 non-bonded parameter combinations
>
> ERROR 1 [file topol.top, line 22752]:
> No default Proper Dih. types
>
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 3 bonded neighbours molecule type 'UNK'
> Excluding 3 bonded neighbours molecule type 'POPC'
>
> NOTE 1 [file topol.top, line 24831]:
> System has non-zero total charge: 14.788998
> Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
>
> There was 1 note
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
> 1388
>
> Fatal error:
> There was 1 error in input file(s)
>
> kindly help
>
>
>
> On Thu, Jul 10, 2014 at 10:17 AM, RINU KHATTRI <nickname.mittu at gmail.com>
> wrote:
>
>> hello gromacs users
>> ohk justin but if unk is deleted then how to put it back in
>> system_inflate.gro
>>
>>
>> On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
>>>
>>>> hello every one
>>>> I am working on complex with popc membrane i did
>>>>
>>>> perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
>>>>
>>>> after this step minimization
>>>>
>>>> grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
>>>>
>>>> i got error
>>>> Fatal error:
>>>> number of coordinates in coordinate file (system_inflated.gro, 10224)
>>>> does not match topology (topol.top, 10245)
>>>> i have been removed 6 lipid molecules in my topology file according to
>>>> output i got one thing new in my system_inflate.gro file the written
>>>> displayed atom is 10224 but after counting it is 10536 so if i correct
>>>> it
>>>> difference is more
>>>>
>>>
>>> I don't know what this means, but the number of atoms that grompp is
>>> finding is going to be correct.
>>>
>>>
>>> in topology file [molecule]
>>>> protein chain 1
>>>> UNK 1
>>>> POPC 122
>>>> how to resolve it
>>>>
>>>
>>> I would venture a guess that UNK has 21 atoms. I don't know that
>>> InflateGRO handles arbitrary molecules, so it may have gotten deleted upon
>>> inflation. Check system_inflated.gro; it will be very obvious if it is
>>> missing.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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>>
>>
>
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