[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Fri Jul 11 08:57:22 CEST 2014
hello gromacs users
thank you justin i got system_shrink.gro after 20 energy minimization and
shrinking next step is solvate your syetem but no command is there the
command is there is
grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA
-nname CL -nn 4
which one is i have to use if both then i do not have system_solv.gro
or system_solv_ions.gro (output)
i have shrinking and minimize structure files
kindly help
On Thu, Jul 10, 2014 at 6:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/10/14, 5:44 AM, RINU KHATTRI wrote:
>
>> 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
>>
>>
> It's not the location within the .top that's the problem, it's the
> contents of the actual restraint .itp file. You made a mistake in creating
> the file, likely including multiple molecules or molecules that are not
> part of the restrained [moleculetype].
>
> -Justin
>
>
> 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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>>>>>
>>>>>
>>>>
>>>>
>>>
> --
> ==================================================
>
> 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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>
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