[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
>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>> --
>>> ==================================================
>>>
>>> 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
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>
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