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.
-Justin
-----Original Message----- From: "Justin Lemkul" <jalem...@vt.edu> Sent: 29/02/2016 15:50 To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>; "Abid Channa" <abid_chann...@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 jalem...@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-requ...@gromacs.org.
