[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Fri Jul 18 09:34:22 CEST 2014
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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>>>
>>>
>>
>
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