Dear Dr. Justin I got your means and it is very helpful for me. Thank you so much :)
Sincerely, Tuong Vy 2015-08-12 21:23 GMT+09:00 Justin Lemkul <[email protected]>: > > > On 8/12/15 8:20 AM, Vy Phan wrote: > >> Dear Dr Justin and Gromacs User, >> As I mentioned in the previous email , I download the parameter from this >> website which was build for all-atom simulation ( >> http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file >> > > The list does not accept attachments, not is it necessary. > > below . I have a confusion with Tielema's website. I use this for run >> membrane protein simulations and it work well, no errors like the topology >> which was embedded in charmm36 force field for with Gromacs format. >> >> > Previous success with a different force field has no bearing on future > success with a different model that uses a different convention (all-atom > vs. united-atom). > > I just want to ask why I got many error when I use the topology which was >> embedded in charmm36 force field for with Gromacs format? Some suggestion >> to me please. >> >> > As I said before, you have serious problems with whatever topology you > managed to generate. A charge of +888 on a 516-lipid DOPC (which is > neutral) is total nonsense, so you certainly have missing or incorrect > atoms that you've bypassed with pdb2gmx options or something else. > Whatever that topology has in it is certainly wrong and should not be used. > > -Justin > > > Dear Dr. Justin >> Thank you so much for your suggestion. I will try with CHARMM-GUI. >> >> Best regards, >> Tuong Vy >> >> 2015-08-12 21:19 GMT+09:00 Vy Phan <[email protected]>: >> >> Dear Dr Justin and Gromacs User, >>> As I mentioned in the previous email , I download the parameter from this >>> website which was build for all-atom simulation ( >>> http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file >>> below . I have a confusion with Tielema's website. I use this for run >>> membrane protein simulations and it work well, no errors like the >>> topology >>> which was embedded in charmm36 force field for with Gromacs format. >>> >>> I just want to ask why I got many error when I use the topology which was >>> embedded in charmm36 force field for with Gromacs format? Some suggestion >>> to me please. >>> >>> Dear Dr. Justin >>> Thank you so much for your suggestion. I will try with CHARMM-GUI. >>> >>> Best regards, >>> Tuong Vy >>> >>> 2015-08-12 20:32 GMT+09:00 Justin Lemkul <[email protected]>: >>> >>> >>>> >>>> On 8/11/15 10:15 PM, Vy Phan wrote: >>>> >>>> Dear Dr. Justin and Gromacs User, >>>>> >>>>> Thank you so much for your helps. >>>>> >>>>> When I use charmm36 ff to generate the topology for lipid (DOPC). I got >>>>> many warning "Warning :Long bond " >>>>> And after get the topology, the total charge is very high (+888 e for >>>>> DOPC >>>>> bilayer have 516 molecular). When I used grompp to generate the .tpr >>>>> file, >>>>> I got the many error like this : >>>>> Error 3379 [file topol_Other_chain_D.itp, line 198252] >>>>> No defaut U-B types >>>>> ... >>>>> Error 2379 [file topol_Other_chain_D.itp, line 98252] >>>>> No default Proper Dih.type >>>>> .... >>>>> >>>>> What can I do to modified the topology to get the correct charge and >>>>> fix >>>>> the error ? >>>>> >>>>> I download dopc.itp from Tieleman's website. I run simulation and all >>>>> things look fine. People have experiences, please tell me the >>>>> difference >>>>> of this topology and the one on the charmm36 force field. >>>>> >>>>> >>>>> The files Tieleman provides are united-atom structures that may use a >>>> different naming convention. They won't have H atoms on the aliphatic >>>> groups and there is no .hdb entry for DOPC. The ridiculous net charge >>>> you >>>> got for DOPC (which is neutral!) should be an indicator that whatever >>>> topology you built is utter nonsense. There should also be no warnings >>>> about missing parameters, so this is further evidence that the topology >>>> is >>>> wrong and the "things look fine" assertion seems totally unfounded to >>>> me. >>>> >>>> If you want to simulate a simple membrane, use CHARMM-GUI to build it. >>>> It will be 100% CHARMM compliant and we give you all the necessary input >>>> files. >>>> >>>> >>>> -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]. >>>> >>>> >>> >>> > -- > ================================================== > > 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]. > -- 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].
