Re: [gmx-users] system has non zero net charge
On 1/8/20 6:01 AM, Yogesh Sharma wrote: Greetings, I am performing membrane protein simulation in the presence of a biomolecule. topology for the molecule was downloaded from ATB server. After simulation run, I found unexpected behviour of the added biomolecule. This ligand named UINL was showing affinity to ASP and GLU residues. ligand didnt seperate through out simulation once bound, which is highly unexpected at neutral pH. Why is that unexpected? Your ligand is Si(OH)4 and likely participates in hydrogen-bonding interactions very easily with charged groups. I was getting these two notes during solvation. Generated 1062 of the 3486 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'U1NL' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... NOTE 1 [file topol2.top, line 18875]: System has non-zero total charge: -1.02 Total charge should normally be an integer. The discrepancy between your value and -1 is simply due to rounding. The larger issue is you have a membrane system with a net charge. If you allow PME to apply a neutralizing background plasma to this system (i.e. you don't use counterions), you will get very severe artifacts. Is it possible this -1 charge is producing artifact. I have addded 20 molecules of same ligand in my system and 6 of them are binding to negative charged residues. I checked total charge on ligand.itp file, its zero. then i checked line 18875 in topol2.top its SOL which is highly unlikely to have any charge. U1NL 3 [ atoms ] ; nr type resnr resid atom cgnr chargemass 1 HS141U1NL H4 10.480 1.0080 2 OEOpt1U1NL O42 -0.814 15.9994 3SI 1U1NL Si 31.336 28.0800 4 OEOpt1U1NL O14 -0.814 15.9994 5 HS14 1U1NL H1 50.480 1.0080 6 OEOpt1U1NL O26 -0.814 15.9994 7 HS14 1U1NL H3 70.480 1.0080 8 OEOpt1U1NL O38 -0.814 15.9994 9 HS141U1NL H2 90.480 1.0080 ; total charge of the molecule: -0.000 How can i check what molecule is throwing this negative -1 charge to my system? POPC is uncharged, water is uncharged, your ligand is uncharged, so the charge must be coming from...? :) -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] system has non zero net charge
Hi Yogesh, this happens to me as well sometimes, there are several options: - your protein is not neutral (my best practice is to you use pdb2gmx interactively and set the charges for all amino acids manually following pkA predictions by e.g. Propka - then you will immediately know if the protien has a charge from the output) - one of your itp files (I guess POPC and U1NL are from ATB) has a non-zero charge - make sure to show 10 decimal points when you calculate the total charge of all the atoms in the ligands, it happens sometimes that these do NOT add up to a completely neutral value, and rounding errors will occur and mess up the total charge of your system - especially if you add 20 identical molecules It is always a good idea to carefully check the parameters obtained from ATB or another server - mistakes happen! - if the charge persists, you must neutralise the system using genion: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genion.html Best of luck Gudrun Am 08.01.2020 um 12:01 schrieb Yogesh Sharma: Greetings, I am performing membrane protein simulation in the presence of a biomolecule. topology for the molecule was downloaded from ATB server. After simulation run, I found unexpected behviour of the added biomolecule. This ligand named UINL was showing affinity to ASP and GLU residues. ligand didnt seperate through out simulation once bound, which is highly unexpected at neutral pH. I was getting these two notes during solvation. Generated 1062 of the 3486 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'U1NL' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... NOTE 1 [file topol2.top, line 18875]: System has non-zero total charge: -1.02 Total charge should normally be an integer. Is it possible this -1 charge is producing artifact. I have addded 20 molecules of same ligand in my system and 6 of them are binding to negative charged residues. I checked total charge on ligand.itp file, its zero. then i checked line 18875 in topol2.top its SOL which is highly unlikely to have any charge. U1NL 3 [ atoms ] ; nr type resnr resid atom cgnr chargemass 1 HS141U1NL H4 10.480 1.0080 2 OEOpt1U1NL O42 -0.814 15.9994 3SI 1U1NL Si 31.336 28.0800 4 OEOpt1U1NL O14 -0.814 15.9994 5 HS14 1U1NL H1 50.480 1.0080 6 OEOpt1U1NL O26 -0.814 15.9994 7 HS14 1U1NL H3 70.480 1.0080 8 OEOpt1U1NL O38 -0.814 15.9994 9 HS141U1NL H2 90.480 1.0080 ; total charge of the molecule: -0.000 How can i check what molecule is throwing this negative -1 charge to my system? Thankyou in advance for your valuable time. -- 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.
