[gmx-users] gmx sasa for protein-ligand complex(problem with command usage)
Dear Gromacs Users,
I have GPCR-protein complex simulation and want to calculate buried surface
area of the complex. I am using gmx sasa but facing problem in using the
command especially the -output part.
I need to calculate SASA for unbound receptor,unbound ligand and of
complex. I have made index file where complex is ofcourse group 1 Protein
and receptor is group 24 and ligand is group 25
when I provide the following command I gt TOTAL SASA
gmx sasa -f .xtc -s .tpr -o bound-sasa.xvg -tu ns -n .ndx -surface 'group
"1"'
but when I add the output part
-output '"hydrophobic" group "1" and charge {-0.2 to 02}; "hydrophilic"
group "1" and not charge {-0.2 to 0.2};
Error in user input:
Selection '"hydrophilic" group "1" and not charge {-0.2 to 0.2}' never
matches
any atoms.
Can anyone tell me how to get SASA for receptor, ligand and compex.
Thanks
Archana
--
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] atomselection for index group of cyclic rings
Hi, First make index file of the atoms involved in rings and then use following command: gmx distance -f .xtc -s .tpr -n .ndx -select 'cog of group " group 1" plus cog of group "group2"' -oav .xvg Hope this helps Thanks Archana On Fri, Apr 17, 2020 at 10:25 AM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > I am interested in measuring the distance between two cyclic rings present > in the residues and ligands over time. Can you kindly suggest how to go > about this? > Specially, if i am interested in measuring the distance between the center > of the two rings over time. Thank you > > -- > Regards, > Prasanth. > -- > 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. > -- 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.
[gmx-users] Theta and gamma angle between tyrosines
Hi, I have to plot theta and gamma angles between tyrosines throughout the simulation to check if they are involved in pi-pi interactions. I have plotted the centroid distance between tyrosines. But don't know which atoms form theta and gamma angle. How to get centroid atom for tyrosine using gromacs? Thanks Archana -- 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] centroid distance for tyrosine
sorry I didn't understood the syntax in first go, I was getting errors as I missed the single quotes but now it worked. gmx distance -f apo-cxcr4-final1.xtc -s mdmodified_cxcr4.tpr -n nter_index.ndx -select 'cog of group "7Y_cog" plus cog of group "12Y_cog"' Thanks On Sun, Feb 17, 2019 at 12:37 AM Justin Lemkul wrote: > > > On 2/16/19 2:01 PM, Archana Sonawani-Jagtap wrote: > > Hi Justin, > > > > I think something is wrong in the command because when I visualize the > > distance between OH atoms of tyrosine's in VMD it shows ranging from 3 to > > 10 ang. Also, when I take single frame in pdb format and check centroid > > distance using PIC webserver, it gives within same range. However, using > > above command it gives distance within 1.37-1.38 ang. > > > > I used following command: > > > > gmx distance -f apo-cxcr4-final1.xtc -s mdmodified_cxcr4.tpr -n > > nter_index.ndx -oav distave_tyr12-21.xvg -select 12Y_cog 21Y_cog -oall > > dist_tyr12-21.xvg > > > > What could be wrong? > > You didn't use the syntax I gave you (and I'm not sure how what you > provided is even a valid command). > > gmx distance is giving you what you asked for, all distances (-oall) in > the groups provided, so you're seeing values that are consistent with > C-C bond lengths. > > -Justin > > > > > > > > > > > On Sat, Feb 16, 2019 at 4:31 AM Justin Lemkul wrote: > > > >> > >> On 2/15/19 2:37 PM, Archana Sonawani-Jagtap wrote: > >>> Hi, > >>> > >>> I want to calculate centroid distance between 2 tyrosine rings > throughout > >>> the simulation. Which option of gmx distance can help to plot the > >> centroid > >>> distance? > >> Create two index groups with the ring atoms, then use gmx distance: > >> > >> gmx distance -s -f -select 'cog of group "ring1" plus cog of group > "ring2"' > >> > >> -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. > >> > > -- > == > > 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. > -- 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] centroid distance for tyrosine
Hi Justin, I think something is wrong in the command because when I visualize the distance between OH atoms of tyrosine's in VMD it shows ranging from 3 to 10 ang. Also, when I take single frame in pdb format and check centroid distance using PIC webserver, it gives within same range. However, using above command it gives distance within 1.37-1.38 ang. I used following command: gmx distance -f apo-cxcr4-final1.xtc -s mdmodified_cxcr4.tpr -n nter_index.ndx -oav distave_tyr12-21.xvg -select 12Y_cog 21Y_cog -oall dist_tyr12-21.xvg What could be wrong? On Sat, Feb 16, 2019 at 4:31 AM Justin Lemkul wrote: > > > On 2/15/19 2:37 PM, Archana Sonawani-Jagtap wrote: > > Hi, > > > > I want to calculate centroid distance between 2 tyrosine rings throughout > > the simulation. Which option of gmx distance can help to plot the > centroid > > distance? > > Create two index groups with the ring atoms, then use gmx distance: > > gmx distance -s -f -select 'cog of group "ring1" plus cog of group "ring2"' > > -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. > -- 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.
[gmx-users] centroid distance for tyrosine
Hi, I want to calculate centroid distance between 2 tyrosine rings throughout the simulation. Which option of gmx distance can help to plot the centroid distance? Thanks, Archana -- 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.
[gmx-users] Calculation for number of ions
Hi all, I want to run simulation of GPCR in POPC bilayer, but the GPCR N-terminal is very flexible and negatively charged whereas the ICL's and C-terminal is highly positively charged. Thus, the they interact with each other during simulation. So, now I want to shield the negative charges of ICL's and C-term by adding ions near this region after neutralising the system. Is there any way to calculate the number of ions required for shielding. I tried physiological conc of 0.154 mole/L using genion command but it adds equal number of Na and CL ions. Any help is appreciated. Thanks, Archana -- 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] SPC water model for CHARMM27FF
Thanks Justin. Will try to use CHARMM36 with TIP3P watermodel. On Sat, Oct 28, 2017 at 11:57 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/28/17 5:49 AM, Archana Sonawani-Jagtap wrote: > >> Dear all, >> >> I have used SPC water model with CHARMM27 forcrfield for performing 100ns >> protein-DNA simulation instead of TIP3P. I wanted to know if SPC water >> model can affect my simulation results in anyway considering many charged >> residues. >> > > Yes, it certainly is. CHARMM specifically balances water interactions > assuming CHARMM-modified TIP3P (with LJ on H atoms) to target individual QM > water interactions. If you change the water model, you potentially > imbalance the entire force field. The water model should generally be > viewed as an integral part of the force field, unless one does a complete > validation that the change in water model does not negatively impact the > target data (water interactions, hydration free energies, helix-coil > equilibrium, etc). > > CHARMM36 is also superior to CHARMM27 and I recommend you use it instead, > particularly if you care about subtle aspects of the DNA structure. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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. > -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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.
[gmx-users] SPC water model for CHARMM27FF
Dear all, I have used SPC water model with CHARMM27 forcrfield for performing 100ns protein-DNA simulation instead of TIP3P. I wanted to know if SPC water model can affect my simulation results in anyway considering many charged residues. Please help me out. Archana Jagtap PhD student 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] GPCR insertion in POPC_Cholesterol bilayer
Thanks for the reply. I have built the bilayer using CHARMM- gui. On Jun 13, 2017 2:20 AM, "Justin Lemkul" <jalem...@vt.edu> wrote: On 6/12/17 4:12 PM, Archana Sonawani-Jagtap wrote: > Hi all, > > I am trying to insert GPCR in POPC with 30 mol% cholesterol bilayer. I am > using Inflategro method for insertion but I found that the script does not > recognize the cholesterol molecules and they are not inflated during the > inflation step. > > If you have more than one lipid type, you have to modify the script to account for this fact. Can anyone please let me know which method to use or I have missed any step? > > Build it online with CHARMM-GUI. -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. -- 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.
[gmx-users] GPCR insertion in POPC_Cholesterol bilayer
Hi all, I am trying to insert GPCR in POPC with 30 mol% cholesterol bilayer. I am using Inflategro method for insertion but I found that the script does not recognize the cholesterol molecules and they are not inflated during the inflation step. Can anyone please let me know which method to use or I have missed any step? Thanks and Regards, Archana Jagtap PhD student NaviMumbai, 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] charmm36 lipid forcefield error
Thanks for solving my error. But then do we need to remove the periodicity of the bilayer obtained from charmm-gui? Regards, Archana On Fri, Jun 2, 2017 at 2:24 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/1/17 4:43 PM, Archana Sonawani-Jagtap wrote: > >> Hi, >> >> I want to perform GPCR simulation in POPC bilayer using Charmm36 >> forcefield. I have generated the bilayer using CHARMM-GUI. I am following >> GPCR tutorial by Justin (modified to GPCR by Anirban). >> >> > CHARMM-GUI gives you the required force field files. Use those and don't > mess with them. > > I want to remove periodicity of the generated bilayer using following >> command: >> >> grompp -f EM.mdp -c popc288.gro -p topol_popc.top -o EM.tpr >> but I am getting below error: >> >> Program gmx grompp, VERSION 5.1 >> >> Source code file: >> /usr/local/gromacs-5.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 312 >> >> Fatal error: >> >> Topology include file "charmm36_lipid.ff/forcefield.itp" not found >> >> I have downloaded Charmm36 FF from gromacs user's section and placed it in >> >> > The force field files on gromacs.org are not authoritative CHARMM36 files > and in fact contain a mixture of force field parameters (C36 for lipids, > but C22+CMAP for protein, if I recall). If you want correct C36 > parameters, get them from our website: > > http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs > > But again, CHARMM-GUI gave you everything you need, from the parent force > field files all the way through the topology of the system, so you > shouldn't have to touch any of this. > > -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. > -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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.
[gmx-users] charmm36 lipid forcefield error
Hi, I want to perform GPCR simulation in POPC bilayer using Charmm36 forcefield. I have generated the bilayer using CHARMM-GUI. I am following GPCR tutorial by Justin (modified to GPCR by Anirban). I want to remove periodicity of the generated bilayer using following command: grompp -f EM.mdp -c popc288.gro -p topol_popc.top -o EM.tpr but I am getting below error: Program gmx grompp, VERSION 5.1 Source code file: /usr/local/gromacs-5.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 312 Fatal error: Topology include file "charmm36_lipid.ff/forcefield.itp" not found I have downloaded Charmm36 FF from gromacs user's section and placed it in /usr/local/gromacs/share/gromacs/top Please help me to solve the error. Thanks Archana Jagtap PhD student 9960791339 -- 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.
[gmx-users] How to calculate number of cholesterol molecules
Hi, I want to perform atomistic simulation in POPC bilayer with 30% cholesterol. So I want to know how to calculate number of cholesterol molecules for 30% concentration? Thanks and Regards, Archana Jagtap PhD student Mumbai, 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.
[gmx-users] g_rdf: normalize by density
Hi, I want to plot g_rdf for peptide and SDS. In many papers I have read *The functions were normalized by the number of atoms in the first selection (peptide atoms) and by a density of 0.01*. 1) I don''t find any option in g_rdf to normalize by density of 0.01. There is one option -[no]norm*yes* (Normalize for volume and density) but no option to put the value 0.01. 2) Does normalized by the number of atoms means to use the below option: -rdf* enum* atom RDF type: atom, mol_com, mol_cog, res_com or res_cog Can anyone please explain. Regards, Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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.
[gmx-users] Gromacs insatallation on centos 6
Hi everyone, I want to install gromacs 4.5.4 on centos 6. Can anyone help me out in this. Thank you. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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.
[gmx-users] TFE-water homogeneous system -NPT
Hello, I am trying to perform peptide simulation using TFE-water system. I did lot of literature search and according carried out NVT for 32ns followed by NPT 10ns simulation for TFE-water system. I found that the TFE get accumulated in the center of the box and water molecules surround them. The system is no more homogeneous. Is this normal or something is going wrong? Any help regarding this is appreciated. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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.
