[gmx-users] Acpype topolgy error
jalemkul at vt.edu
Mon Feb 29 14:06:49 CET 2016
On 2/29/16 7:56 AM, Mutemi Chief wrote:
> Just change ca to C ie carbon. Pay attention to the atomic masses indicated
I would strongly advise against doing this, unless it is 100% certain that C and
ca have equivalent bonded and nonbonded parameters. The acpype topology should
include all necessary parameters. Only if the user has altered the topology
would an error arise.
> -----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 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
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