[gmx-users] error in grompp command

[Justin Lemkul]

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 at 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 at 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

==================================================