[gmx-users] Error in Coarse Graining the atomistic trajectory

of how to troubleshoot the above problem. Any help will be highly appreciated. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged

Re: [gmx-users] Martini Website is not accessible

Okay, Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Mon, May 22, 2017 at 5:17 PM, Peter Kroon wrote: > Hi, > > > we are aware of it and will probably fix it later today. It's an update > gone wrong.

[gmx-users] Martini Website is not accessible

*Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission

[gmx-users] Error In Umbrella sampling.

the tutorial. Is is safe to use maxwarn in this case ? or is their any solution to overcome this warning ? Any help will be highly appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thanks a lot! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 9:10 PM, Justin Lemkul wrote: > > > On 2/23/17 9:07 AM, Anurag Dobhal wrote: > >> Dear Justin, >>

Re: [gmx-users] Potential Energy is positive on minimizing the system

*Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Thank you ! > > > > > *Anurag Dobhal* > *G

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thank you ! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul wrote: > > > On 2/23/17 8:29 AM, Anurag Dobhal wrote: > >> Thank you. Should I n

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thank you. Should I not use PME and PBC while performing simulations in Vaccum ? -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or oth

[gmx-users] Potential Energy is positive on minimizing the system

Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Any help will be appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or ent

[gmx-users] Potential Energy is positive on minimizing the system

Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Any help will be appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity

Re: [gmx-users] Neutralization of the non solvated system

Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Dec 22, 2016 at 6:26 PM, Justin Lemkul wrote: > > > On 12/22/16 5:24 AM, Anurag Dobhal wrote: > >> Dear Gromacs users, >> >> I am simu

[gmx-users] Neutralization of the non solvated system

Dear Gromacs users, I am simulating a polyemer chain having positive charge. I am running the simulation without any solvent, in this sitiuation how can I neutralize my system ? Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai

[gmx-users] Invalid order for directive molecules

your help. Thanks and Regards *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged materia

Re: [gmx-users] Regarding tc-grps

Thank you Justin and Peter for the valuable inputs. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Sep 29, 2016 at 8:25 PM, Peter Kroon wrote: > Hi, > > please see http://www.gromacs.org/Documentation/Terminology/Th

Re: [gmx-users] Regarding tc-grps

stoping, showing error of segmentation fault. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Sep 29, 2016 at 8:26 PM, Justin Lemkul wrote: > > > On 9/29/16 10:31 AM, Anurag Dobhal wrote: > >> Dear Grom

[gmx-users] Regarding tc-grps

Dear Gromacs users, I am simulating a polymer chain without any solvent using OPLS AA force field, how many tc-grps should I put in the .mdp file ? as there is only one 1 group in the topol.top file. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical

Re: [gmx-users] changing the location of a molecule in a box

protien. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* On Fri, Sep 9, 2016 at 4:24 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear Gromacs users, > > I am working on a biphasic system where I have taken chloroform and water >

[gmx-users] changing the location of a molecule in a box

protien. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other

[gmx-users] Parameters file for CHARMM 27 Force Field

-Vz79yKJWFgwYVN3cUJHSUE Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any

Re: [gmx-users] Energy minimization has stopped

Thanks a lot Justinn and Mark for the valuable suggestions. I will start over again by choosing a force field which is suitable for the RNA molecules. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun

Re: [gmx-users] Energy minimization has stopped

RNA molecules. I was suggested (Link Below) earlier that I can take the charges from any other forcefield. (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) please enlight me where I am going wrong. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology

Re: [gmx-users] Energy minimization has stopped

I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote

[gmx-users] Energy minimization has stopped

f rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) any suggestions ? *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the per

[gmx-users] WARNING: Duplicate line found in or between hackblock and rtp entries

Dear Gromacs Users, I Simulated a Nucleotide pair using OPLS AA force field. while running " gmx pdb2gmx" I am getting the following warning. WARNING: Duplicate line found in or between hackblock and rtp entries How to address this warning ? Thank You *Anurag Dobhal* *Gradua

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Fri, Jun 17, 2016 at 5:02 PM, Justin Lemkul wrote: > > > On 6/17/16 6:26 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >&

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

Dear Justin, I have already added the H to the guanine molecule striped from the nucleotide. The charges given in the ffnonbonded.itp for all the atoms of guanine (Including the H on N9) do not add to zero. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical

[gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

at guanine has negative charge ? should I continue with thae same parameters or change them to bring the total charge of the molecule to zero. Thank You for your help *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIME

Re: [gmx-users] Grompp error

Thanks a lot for your insight. I will redefine them. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 30, 2016 at 8:26 PM, Justin Lemkul wrote: > > > On 5/30/16 10:55 AM, Anurag Dob

Re: [gmx-users] Grompp error

Thanks a lot for your reply. I have set tc-groups as tc-grps = Other acetone ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each *Anurag Dobhal* *Graduate Student (Bioprocess Technology

[gmx-users] Grompp error

ell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet Fatal error: Atom 79 in multiple T-Coupling groups (1 and 2) " The error means that T-coupling is treating both the polymer (other) and solvent (acetone) as other molecules. How can I rectify the error ? *An

Re: [gmx-users] uninstall gromacs 5.0

Thank a lot Mark and Sun for your valuable suggestions. The problem is solved. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 23, 2016 at 10:43 PM, sun wrote: > I am sorry for so man

[gmx-users] uninstall gromacs 5.0

Dear Users: I want to uninstall gromacs 5.0 and replace it with gromacs 5.1. The link provided in the gromacs website (Removing a GROMACS installation) does not give any solution with the same. how can i uninstall gromacs 5.0 ?? Thanks in advance. Anurag Dobhal -- *DISCLAIMER:* *This

[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error "No default Ryckaert-Bell. types". I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default Ryckaert-Bell. types. but on checking ffbond

[gmx-users] Grompp error "No default Ryckaert-Bell. types"

Hello all How can I address the "No default Ryckaert-Bell. types error". The error is also in between the atoms which are not bonded with each other. Thank you -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidentia

[gmx-users] Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database

Dear all I am running pdb2gmx to creat the topology file of my structure, But I did get the error Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database Although my .pdb file does not contain Atom type Zn2+ (residue ZN) *Anurag DobhalJuniour Research fellowSupervisor: D

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

Thank a lot Justin for your help and time. Thank you On Fri, Oct 3, 2014 at 5:21 PM, Justin Lemkul wrote: > > > On 10/3/14 7:48 AM, Anurag Dobhal wrote: > >> How to iteration the system 26 times. I am unable to understand that part. >> >> please explain how to do

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

How to iteration the system 26 times. I am unable to understand that part. please explain how to do it. Thank you On Fri, Oct 3, 2014 at 3:51 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > hello Justin thanks for your reply. > > I am unable to understand how to

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

file ) and what will be the command ??? looking for your kind reply. please help. Thank you On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul wrote: > > > On 10/2/14 12:51 PM, Anurag Dobhal wrote: > >> how will I get to know that the system have shrunken enough, and which

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

how will I get to know that the system have shrunken enough, and which file I need to solvate. On Thu, Oct 2, 2014 at 9:16 PM, Justin Lemkul wrote: > > > On 10/2/14 8:50 AM, Anurag Dobhal wrote: > >> Thanks Justin >> >> I m running the command >> >>

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

1956) can you please help what caused this error. Thanking you On Tue, Sep 30, 2014 at 8:05 PM, Justin Lemkul wrote: > > > On 9/30/14 10:30 AM, Anurag Dobhal wrote: > >> Dear justin >> >> Thank you for your rely and precious time. >> >> I am aware t

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

onfout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Please help. On Tue, Sep 30, 2014 at 4:41 PM, Justin Lemkul wrote: > > > On 9/30/14 7:06 AM, Anurag Dobhal wrote: > >> Thank you Justin for your reply >> >>

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul wrote: > > > On 9/30/14 5:51 AM, Anurag Dobhal wrote: > >> Hello gromacs users. >> >> >> I am running GROMACS Tutorial of KALP15 in DPPC. >> >> I am in the step define box

[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*)

Re: [gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

hello justin Can you please tell me how will i solvate my system. which command will i use and what will be my input and output file. Thanks for your help Anurag dobhal On Sun, Sep 28, 2014 at 6:58 PM, Justin Lemkul wrote: > > > On 9/28/14 9:14 AM, Anurag Dobhal wrote: > >>

Re: [gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

On Sun, Sep 28, 2014 at 6:33 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear users. > > > I am doing the tutorial "KALP15 in DPPC". > > I heve done till the command > > perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 a

Re: [gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

uot;confout.gro" please help how to proceed and where I am wrong. Thank you Anurag Dobhal On Sun, Sep 28, 2014 at 5:37 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear users. > > > I am doing the tutorial "KALP15 in DPPC". &

[gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

in easy words how to proceed. Please help Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you

[gmx-users] Regarding siRNA simulation.

I am simulating an RNA molecule in which first residue has a 5'-PO4 cap, which is uncommon. I am adding the atoms and bond parameters in the .rtp files in the existing force field directories but these parameters are not getting saved. I am using Amber 99 force field and i am making changes in the

[gmx-users] Regarding error in grompp while running the tutorial of " KALP15 in DPPC "

I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown atomtype OW please help !!! -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain c

[gmx-users] regarding gromacs installation

steps are enough to install gromacs or do i need to do some thing more. please help. Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review

[gmx-users] Regarding error in grompp while running the tutorial of " KALP15 in DPPC "

I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown bond_atomtype MNH3 please help -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may conta

[gmx-users] Regarding error in grompp while running the tutorial of " KALP15 in DPPC "

I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown bond_atomtype MNH3 -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidentia