[gmx-users] Error in system_inflate.gro coordinates does not match

RINU KHATTRI nickname.mittu at gmail.com
Sat Jul 19 06:37:35 CEST 2014


hello everyone
ok justin but i used DSTRONG_POSERES in topology not the STRONG_POSERES
and -DSTRONG_POSERES
ok i will try to send the image
kindly check my tolpology is it ok
thanks in advance


On Fri, Jul 18, 2014 at 4:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/18/14, 3:34 AM, RINU KHATTRI wrote:
>
>> hello justin images can not be sent by this email address (gmx--) i am
>> helpless how can i send it  to you (protein is out side the lipid
>> membrane )
>> thank you
>>
>>
> Upload images to a file-sharing service and post the links to the images.
>
> -Justin
>
>
>
>> On Fri, Jul 18, 2014 at 1:01 PM, RINU KHATTRI <nickname.mittu at gmail.com>
>> wrote:
>>
>>  hello gromacs users
>>> i saw my em.log file after minimization no position restrain term is
>>> there
>>> even i used -D  flag
>>> ; Include Position restraint file
>>> #ifdef POSRES
>>> #include "posre.itp"
>>> #endif
>>> ; Strong position restraints for InflateGRO
>>> #ifdef  -DSTRONG_POSRES
>>> #include "strong_posre.itp"
>>>
>>> #endif
>>> ; Strong position restraints for InflateGRO
>>> #ifdef  -DSTRONG_POSRES
>>> #include "backbone_posre.itp"
>>>
>>> #endif
>>>
>>> ; Include ligand topology
>>> #include "drag.itp"
>>>
>>> ; Ligand position restraints
>>> #ifdef -DPOSRES_UNK
>>> #include "posre_UNK.itp"
>>> #endif
>>>
>>>
>>> ; Include POPC chain topology
>>> #include "popc.itp"
>>>
>>> ; Include water topology
>>> #include "gromos53a6_lipid.ff/spc.itp"
>>>
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ;  i funct       fcx          fcy             fcz
>>>     1    1       1000000    1000000    1000000
>>>     2    2       1000000    1000000    1000000
>>>     3    3       1000000    1000000    1000000
>>> #endif
>>>
>>> ; Include topology for ions
>>> #include "gromos53a6.ff/ions.itp"
>>> this my topology how can i put position restrain
>>>   minim.mdp
>>> define          = -DSTRONG_POSRES   -DSTRONG_POSRES   -DSTRONG_UNK
>>>
>>> kindly help
>>>
>>>
>>> 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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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
> --
> ==================================================
>
> 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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