[gmx-users] Error in system_inflate.gro coordinates does not match

RINU KHATTRI nickname.mittu at gmail.com
Thu Jul 10 07:16:49 CEST 2014

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
-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

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
  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:

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>

> 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.

More information about the gromacs.org_gmx-users mailing list