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

RINU KHATTRI nickname.mittu at gmail.com
Sat Jul 19 15:56:17 CEST 2014


hello everyone
i know justin -D is for minim.mdp not for topology i used simply D
still it is not working
kindly help


On 7/19/14, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/19/14, 12:37 AM, RINU KHATTRI wrote:
>> hello everyone
>> ok justin but i used DSTRONG_POSERES in topology not the STRONG_POSERES
>> and -DSTRONG_POSERES
>
> Simply put, that's the wrong syntax.  #ifdef statements should not be
> prefixed
> by -D.  This is what is correct (and what is specified in the tutorial):
>
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> -Justin
>
>> 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
>>>>>>>>
>>>>>>>> * Please search the archive at http://www.gromacs.org/
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>>>>>>>> or
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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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>>>
>
> --
> ==================================================
>
> 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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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