Dear Justin, Yes, the problem is with the blank line at the end of atomtypes.atp. Now its working fine. I have added the missing dihedral types from other sources.
I have compared the cholesterol CHARMM parameters that are converted to gromacs format and original parameters from "toppar_all36_lipid_cholesterol.str" file available in CHARMM website. I found some variations in the atom types. For eg., The atom type of C3 atom from sterol ring in cholesterol is CTL1 in CHARMM whereas it is CG311 in charmm36-Nov2014.ff. On Thu, Nov 6, 2014 at 6:21 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/6/14 12:45 AM, Venkat Reddy wrote: > >> Dear Justin, >> Thanks for the update. But unfortunately I couldn't find the parameters >> for >> cholesteryl oleate. So, I tried to convert again the parameters from >> CHARMM >> to GROMACS using these updated files: >> >> ./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf >> /usr/local/gromacs/share/gromacs/top/charmm36-nov2014.ff >> >> Here I am getting an error like, >> >> Traceback (most recent call last): >> File "./cgenff_charmm2gmx.py", line 778, in <module> >> atomtypes = read_gmx_atomtypes(atomtypes_filename) >> File "./cgenff_charmm2gmx.py", line 71, in read_gmx_atomtypes >> var = [entry[0],entry[1]] >> IndexError: list index out of range >> >> If I use the charmm36 files uploaded in March 2014, Its not throwing any >> error. Is there something wrong in the updated files? >> >> > Possibly. There is a blank line at the end of atomtypes.atp - does the > error go away if you delete this blank line? > > Also note that you don't need to re-convert your topology; what I was > suggesting was that the new force field files cover more parameters for > lipids, so if the needed dihedral is present (I can't actually say because > you only provided two of the atom types) then your topology should work > without any changes. > > > -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 > > [email protected] | (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 [email protected]. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 [email protected].
