On 4/12/16 2:22 PM, Brier, Troy wrote:
To whom it may concern, I am attempting to run a single protein in water Martini coarse grain simulation. I used martinize.py (version 2.4) to coarse grain the protein and add a dilsulfide bond. When attempting to run the minimization phase (I am using Gromacs version 5.1) I receive the following error: Fatal error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors After troubleshooting I determined the error came from the Bonds section in the Protein_A.itp file produced from martinize.py, and specifically from the section having to do with the disulfide bonds. The error seems to be related to martinize.py determining the bond constraints of the disulfide bone to not match those of the literature values, and the script prints the following message: Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol. So I changed the section in the Protein_A.itp file from: (Error Causing Protein_A.itp file under [bonds]) ; Links/Cystine bridges 253 281 1 0.24000 to: (Error Causing Protein_A.itp file under [bonds]) ; Links/Cystine bridges 253 281 1 0.39000 5000 and then the minimization step runs without the fatal error. What I would like to know if making this change is the proper thing to do or should I keep the constraint distance at 0.24 nm and just add in the bond strength of 5000 kJ/mol?
The wording of the error message states that it's supposed to be a constraint (i.e. fixed distance), not a harmonic interaction. So if it's a constraint, it's simply being written to the wrong section of the topology. It may be better to post this question to the MARTINI forum. A difference between a rigid 0.24 nm distance and a harmonic 0.39 nm distance is quite substantial.
-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.