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

Justin Lemkul jalemkul at vt.edu
Fri Jul 18 12:41:35 CEST 2014 


On 7/18/14, 6:38 AM, RINU KHATTRI wrote:
> hello every one
> i am still in minimization step i thing i notice is -DSTRONG_POSERES is not
> working even i added DSTRONG_POSERES in topology file

Because you've made a typo.  -DSTRONG_POSERES will not trigger the STRONG_POSRES 
block.

-Justin

> i simpley used DPOSERES it workks in log file value is there
> Energies (kJ/mol)
>             Bond        G96Bond          Angle       G96Angle    Proper Dih.
>      9.72432e+02    6.12232e+02    8.77917e+03    3.71444e+03    7.92883e+03
>   Ryckaert-Bell.  Improper Dih.          LJ-14     Coulomb-14        LJ (SR)
>      3.99236e+03    1.80953e+03    4.62776e+03    6.46567e+04   -1.53213e+04
>     Coulomb (SR)   Coul. recip. Position Rest.      Potential Pressure (bar)
>     -3.95141e+04   -1.46181e+05    4.32569e+02   -1.03490e+05
> 0.00000e+00
> still protein is out
>
> inflated.gro is ok but minimization step it is out
> kindly help
>
>
> On Fri, Jul 18, 2014 at 1:04 PM, RINU KHATTRI <nickname.mittu at gmail.com>
> 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
>>
>>
>> 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

==================================================

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