[gmx-users] Acpype topolgy error

[Mutemi Chief]

Just change ca to C ie carbon. Pay attention to the atomic masses indicated 

-----Original Message-----
From: "Justin Lemkul" <jalemkul at vt.edu>
Sent: ‎29/‎02/‎2016 15:50
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>; "Abid Channa" <abid_channa04 at yahoo.com>
Subject: Re: [gmx-users] Acpype topolgy error



On 2/29/16 4:51 AM, Abid Channa wrote:
> Dear Gromacs users,
> I am going to run complex simulation. I have prepared ligand topology through acpype , from where I have taken two files .gro and .itp file. I have used Gromos ff for my simulation . I got atom type error while running this command  " gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr". My acpype taken .itp file is like [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
>       1   ca     1   THA    C1    1    -0.119000     12.01000 ; qtot -0.119
>       2   ca     1   THA    C2    2    -0.173300     12.01000 ; qtot -0.292
>       3   ca     1   THA    C3    3     0.430600     12.01000 ; qtot 0.138
>       4   ca     1   THA    C4    4    -0.182300     12.01000 ; qtot -0.044
>       5   ca     1   THA    C5    5    -0.105000     12.01000 ; qtot -0.149It gave following error
> Fatal error:
> Atomtype ca not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Kindly suggest me How can I resolve this problem.
>

There are probably new [atomtypes] in the topology that you haven't included. 
Atom types are case-sensitive and lowercase types are often used to avoid 
conflicts with the parent force field.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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