[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Fri Jul 11 09:18:52 CEST 2014
hello
i am following the lysozyme tutorial
editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0
solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
but after running second command i got error solvate command not found
gmx solvate is also not working
On Fri, Jul 11, 2014 at 12:27 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:
> 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
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/
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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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