ie. do the replacement on your input coordinate file, not the .rtp!
On Tue, Jun 17, 2014 at 10:35 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 > and HB3 and use sed (or your text editor) to do the replacement. > > Mark > > > On Tue, Jun 17, 2014 at 8:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 6/17/14, 1:51 PM, Matthew Stancea wrote: >> >>> Dr. Justin Lemkul, >>>>> >>>>> Ah I see. I also noticed that in the original specbond.dat, the bond >>>>>>> distance specification for the disulfide bonds between 2 CYS's or >>>>>>> between 2 >>>>>>> CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I >>>>>>> still find a bit unclear is the final columns (residue rename). Is this >>>>>>> what my specbond.dat file should look like? >>>>>>> >>>>>>> >>>>>> The final columns specify the new residue names that should be >>>>>> assigned to the >>>>>> residues only in the case that a special bond was created. You'll >>>>>> see from the >>>>>> existing Cys specifications that a residue named "CYS" (standard PDB >>>>>> nomenclature for any Cys residue) is converted into the .rtp-specific >>>>>> CYS2, but >>>>>> only if a special bond is created. The nomenclature exists because >>>>>> of the way >>>>>> the force fields work. In your case, you don't need to rename >>>>>> anything, so >>>>>> preserving the original residue names is the proper way to go. >>>>>> >>>>> >>> Of course, the answer to "is this correct?" is generally obtained by >>>>>> running it ;) >>>>>> >>>>> >>> 3 >>>>>>> CYS N 1 VAL C 1 0.132 CYS VAL >>>>>>> CYS SG 1 CYS SG 1 0.20 CYS2 CYS2 >>>>>>> CYM SG 1 CYM SG 1 0.20 CYS2 CYS2 >>>>>>> >>>>>> >>> With the above specbond.dat file in the working directory, I attempted >>>>> the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o >>>>> conf.gro >>>>> -p topol.top -i kalata.itp" and received this fatal error message (it is >>>>> the same as the original): >>>>> >>>> >>> ------------------------------------------------------- >>>>> Program pdb2gmx_mpi, VERSION 4.6.2 >>>>> Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, >>>>> line: 727 >>>>> >>>>> Fatal error: >>>>> Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms >>>>> while sorting atoms. >>>>> >>>>> For a hydrogen, this can be a different protonation state, or it >>>>> might have had a different number in the PDB file and was rebuilt >>>>> (it might for instance have been H3, and we only expected H1 & H2). >>>>> Note that hydrogens might have been added to the entry for the >>>>> N-terminus. >>>>> Remove this hydrogen or choose a different protonation state to solve >>>>> it. >>>>> Option -ignh will ignore all hydrogens in the input. >>>>> For more information and tips for troubleshooting, please check the >>>>> GROMACS >>>>> website at http://www.gromacs.org/Documentation/Errors >>>>> ------------------------------------------------------- >>>>> >>>>> >>> Your input coordinate file does not conform to the required >>>> nomenclature of the >>>> >>> force field. The error message says it all. >>> >>> So according to the error message, it says that I can remove the HB3 >>> from the rtp entry NCYX. I was able to locate that to at least one file: >>> "residues.xml". >>> >>> Will editing that file (while backing up the original of course) allow >>> me to bypass this error? For example, if I manually edit that file so that >>> rtp entry NCYX contains all the atoms and only the atoms I want my initial >>> atom to have, can pdb2gmx use that file in that way? >>> >>> >> No, absolutely not. You should never modify the force field files in >> such a way. The force field has expected nomenclature. You must make your >> coordinate file match that nomenclature, not the other way around. If you >> start removing atoms from the .rtp file, your whole setup will be junk. >> >> The simple answer here has already been printed by pdb2gmx. Use -ignh to >> have the H atoms built back onto the structure and magically named >> correctly. >> >> >> -Justin >> >> -- >> ================================================== >> >> 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 >> >> 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? 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