Re: [gmx-users] Unstable system [was: (no subject)]
Please remember to use a sensible subject line. On 10/15/14 6:53 AM, Padmani Sandhu wrote: Hello I have energy minimized the complex successfully and I dont understand whats wrong with the system. What were Epot and Fmax from minimization? Please copy and paste the actual output. What force field are you using? What is the source of your ligand parameters? -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.
Re: [gmx-users] Unstable system [was: (no subject)]
Hello Justin, Epot = -3.4264112e+07 Fmax= 8.5767386e+02 from energy minimization. I am using force field Gromos43a1 and ligand parameters were derived from PRODRG. I have also minimized same protein-ligand complex in the water ealier. Regards, Padmani On Wed, Oct 15, 2014 at 5:05 PM, Justin Lemkul jalem...@vt.edu wrote: [image: Boxbe] https://www.boxbe.com/overview This message is eligible for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DJxBYyH2EjvMPxiRvbn3FhkLhAGVmf0%252FglgaadAaAuZ22xg9m82xiDA%252BfryAH%252BzN%252BHQj0hoXdZFWmmsEyMpxtxSjQ%252BpWJOj7NwQcbT71h3kiqInK5iGsb3EAW3kkfPdwsswC0w2wyASM%253D%26key%3DZJnPJqjmAD0XHnStRzL68jXzi0Hu3B%252F%252B7ghd%252BWNiMIg%253Dtc_serial=18953694948tc_rand=2029571302utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 | More info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=18953694948tc_rand=2029571302utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 Please remember to use a sensible subject line. On 10/15/14 6:53 AM, Padmani Sandhu wrote: Hello I have energy minimized the complex successfully and I dont understand whats wrong with the system. What were Epot and Fmax from minimization? Please copy and paste the actual output. What force field are you using? What is the source of your ligand parameters? -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. -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- 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.
Re: [gmx-users] Unstable system [was: (no subject)]
I have also carried out MD simulation for the same comlex in water and that worked perfectly. On Thu, Oct 16, 2014 at 1:50 AM, Justin Lemkul jalem...@vt.edu wrote: [image: Boxbe] https://www.boxbe.com/overview This message is eligible for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3Dcn7kjseE1qsZ3%252Fyd7n0%252FnivMrWPikx9abmED9c1Z42zTxtJsdJ4Nlq8B1dPjg96fP9AJ16aIbU8Kj7OnCGkj2WcFizgzmQOxfGDp41XzFi%252FbKCndwpcMOGrzAQcBkfgtR1XTfCbCQOE%253D%26key%3DO1Af6fqB%252BADty4CrThw297lFG47eK14mpIp97%252FGkvi0%253Dtc_serial=18958403331tc_rand=66307849utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 | More info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=18958403331tc_rand=66307849utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 On 10/15/14 12:35 PM, Padmani Sandhu wrote: Hello Justin, Epot = -3.4264112e+07 Fmax= 8.5767386e+02 from energy minimization. Seems reasonable. I am using force field Gromos43a1 and ligand parameters were derived from PRODRG. PRODRG produces topologies full of errors. Have you done any manual adjustments to improve the quality of the topology? I have also minimized same protein-ligand complex in the water ealier. So minimization works, but does an MD simulation work? That will help sort out whether or not the issue is related to the membrane. -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. -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- 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.
