[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Sat Jul 19 06:37:35 CEST 2014
hello everyone
ok justin but i used DSTRONG_POSERES in topology not the STRONG_POSERES
and -DSTRONG_POSERES
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/
>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list