[gmx-users] error in grompp command

[RINU KHATTRI]

hello everyone
my grompp related   problem atomtype CA not found has been solved now i am
using 56a3 force field for protein ligand complex with popc but srill i
didnt get em.tpr a new error



Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (popc128.gro, 14036)
             does not match topology (topolpopc.top, 17459)
kindly help



On Wed, Jul 2, 2014 at 3:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/2/14, 6:07 AM, RINU KHATTRI wrote:
>
>> hello gromacs users
>>   i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the
>> place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are
>> present according to tutorial i have been followed  all the step
>> still em.tpr not formed
>> atomtype CA not found
>>
>>
> "CA" is the gmx.ff nomenclature for the calcium type, so that suggests
> you're mixing and matching force fields (note that gmx.ff has been removed
> from the latest Gromacs version, since it should not be used).  Without
> explicit detail of your topology (i.e. post your files so they can be
> downloaded), there's very little that can be done to suggest where things
> have gone wrong.  I strongly suspect you've mixed and matched force fields
> somewhere, which is easy to do when dealing with complex systems.  Pick a
> force field, stick to it exactly.
>
> -Justin
>
>
>
>> On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. <
>> valentina.erastova at durham.ac.uk
>>
>>> wrote:
>>>
>>
>>  Hi Rinu,
>>>
>>> See what forcefield files you include in your topology, then go to the
>>> force field folders and check if those indeed have that atom types.
>>> You must indeed be missing the CA type. Likely, you just forgot to
>>> include
>>> some topology file.
>>>
>>> V
>>>
>>>
>>>
>>>
>>> On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-request@
>>> maillist.sys.kth.se
>>> <mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Wed, 2 Jul 2014 12:26:07 +0530
>>> From: RINU KHATTRI <nickname.mittu at gmail.com<mailto:
>>> nickname.mittu at gmail.com>>
>>> To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
>>> Subject: [gmx-users] error in grompp command
>>> Message-ID:
>>> <CAOEfx3KBphAK_BRP4L4orCp_gSBsuSOHNLUgHX0WyJweWuaN9A at mail.gmail.com
>>> <mailto:CAOEfx3KBphAK_BRP4L4orCp_gSBsuSOHNLUgHX0WyJweWuaN9A@
>>> mail.gmail.com
>>>
>>>>
>>>>>  Content-Type: text/plain; charset=UTF-8
>>>
>>> hello gromacs
>>> i an working on protein ligand complex with lipid membrane (popc)
>>>
>>> grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn
>>> -1
>>>
>>> after this fatal error atomtypes CA not found
>>> and only md.oonly mdout is formed
>>> kindly help
>>>
>>>
>>> ------------------------------
>>>
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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
>
> ==================================================
>
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