[gmx-users] Building and Equilibrating a United-Atom DOPC-DPPC-Cholesterol Bilayer

Hello all, I have been attempting to build a proper united-atom DOPC-DPPC-Cholesterol bilayer for use in simulations for a while. At first I used CHARMM-GUI and then backward after equilibration to convert the coarse-grained equilibrated bilayer into a UA representation, but the resulting membra

Re: [gmx-users] problems in MPI run for REMD in GROMACS

On Tue, May 3, 2016 at 2:50 PM, Pabitra Mohan wrote: > Dear Gromacs Users, > Can any body suggest the solutions to my problem appearing during REMD run > in GROMACS > > While executing the following command these error messages are coming > > pabitra@pabitra-Dell-System-XPS-L502X:~/Desktop/ctld_r

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 4

Dear users, Got it. I was running REMD in my laptop with 8 processors but tried in HPCC with 20 processors and its running. Thank you very much for your suggestions On Tue, May 3, 2016 at 1:53 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing li

[gmx-users] cisplatin charmm36 parameter

Dear all, im looking for cisplatin(https://en.wikipedia.org/wiki/Cisplatin) c36 parameter,i tried https://cgenff.paramchem.org/ ,but it says problem with Pt in the molecule.so can anyone tell me where i can get parameters for cisplatin ?! .. i know we can make using Force field tool kit in VMD

[gmx-users] Residue not found in residue topology database

Dear All I have a structure file(.pdb) of single cellulose chain with Residue type GLCB (beta-D-glucopyranosyl). I try to run the structure file with pdb2gmx command and found this error. "Fatal error: Residue 'LCB' not found in residue topology database". I am not sure why my residue GLCB is sho

Re: [gmx-users] Residue not found in residue topology database

Hi, Usually this means you've edited the PDB file and broken its fixed-column format, so that the code only sees the "LCB" part of your intended residue name. You can use four columns starting from the one you can see in your original file, but you can't start the name from a column to the left.

[gmx-users] simulation in urea

Dear All, I am using amber99sb for simulation. While generating topology file for urea I am getting following error for hydrogens in urea molecule gmx pdb2gmx -f sol-d.pdb -o protein1.gro -p topol1.top -ignh - WARNING: atom H11 is missing in residue URE 1914 in the pdb file You might ne

[gmx-users] Starting residue "XXX"in chain not identified as Protein/RNA/DNA.

Dear All I have a structure file(.pdb) of single cellulose chain with Residue type GLCB (beta-D-glucopyranosyl). I try to run the structure file with pdb2gmx command and found this error. I also attached the pdb file which i used. " Using default: not generating all possible dihedrals Using defau

Re: [gmx-users] Starting residue "XXX"in chain not identified as Protein/RNA/DNA.

Hi, Answer is here itself Starting residue UN15 in chain not identified as Protein/RNA/DNA.Warning: Starting residue UN17 in chain not identified as Protein/RNA/DNA.* check the chain UN17 and define what it is ,please check in the mailing list also ,there are lots of thread regarding this. --

Re: [gmx-users] cisplatin charmm36 parameter

There are Pt parameters available in CHARMM, from: H. Heinz, R. A. Vaia, B. L. Farmer and R. R. Naik, Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials, J. Phys. Chem. C, 2008, 112,17281-17290. These parameters were, of c

[gmx-users] Relative binding free energy from a neutral to a charged molecule

Dear Users, I’m trying to perform relative binding free energy calculations for the transformation from a neutral to a charged molecule. I know reading several articles that this kind of transformations are affected by artifacts due to the used effective electrostatic interaction function and a

[gmx-users] gmx hbond - specify precise atom names involved

Hi all, Can gmx hbond accept user specified atoms for the donors (default OH and NH) and acceptor (default O and N)? I don¹t seem to find any mention of this in the -help text. I have a post-trans modified protein from a rather bulk cross-linked peptide chain. I defined unique atom times but I h

[gmx-users] unsuscribe

unsuscribe -- *Ire* -- 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/

[gmx-users] Fw: MDsimulation of Protein-DNA complex

From: "soumi "Sent: Tue, 03 May 2016 19:21:47To: Subject: MDsimulation of Protein-DNA complexDear All, I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN force field with gromacs.In order to neutralize the net cha

[gmx-users] Fw: MDsimulation of Protein-DNA complex

From: "soumi "Sent: Tue, 03 May 2016 19:24:22To: Subject: Fw: MDsimulation of Protein-DNA complexFrom: "soumi "Sent: Tue, 03 May 2016 19:21:47To: Subject: MDsimulation of Protein-DN

[gmx-users] MDsimulation of Protein-DNA complex

Dear All, I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN force field with gromacs.In order to neutralize the net charge on the protein-DNA complex by adding the correct number of  positive ions or negative ions  I have used the following command in gromacs

Re: [gmx-users] gmx hbond - specify precise atom names involved

On 5/3/16 9:16 AM, Nash, Anthony wrote: Hi all, Can gmx hbond accept user specified atoms for the donors (default OH and NH) and acceptor (default O and N)? I don¹t seem to find any mention of this in the -help text. It's hard-coded in the source, so it's rather inflexible. I have a post

Re: [gmx-users] unsuscribe

Please refer to the links provided at the bottom of every message that comes across the list: * 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. On 5/3/16 9:24 AM, Wood Irene wrote: unsuscri

Re: [gmx-users] MDsimulation of Protein-DNA complex

Hi, What you have described is no physical. You should avoid doing that unless you have a better reason. In normal MD, counter ions don't need special treatment such as restraint to some solute. Regards Terry > On 3 May 2016, at 9:51 PM, soumi wrote: > > Dear > All, > I am wor

[gmx-users] pdb2gmx assign CSER to non-terminal serine

Hi Gromacs Users, I'm using pdb2gmx to process my pdb files with a phospho-tyrosine using amber99sb-ildn.ff. The relavant content in my pdb looks like this (There is a serine before phosphorylated tyrosine): ATOM202 N SER26 31.593 -68.669 -25.834 1.00208.96 N ATOM203 CA S

Re: [gmx-users] pdb2gmx assign CSER to non-terminal serine

On 5/3/16 12:02 PM, Zheng Ruan wrote: Hi Gromacs Users, I'm using pdb2gmx to process my pdb files with a phospho-tyrosine using amber99sb-ildn.ff. The relavant content in my pdb looks like this (There is a serine before phosphorylated tyrosine): ATOM202 N SER26 31.593 -68.669

Re: [gmx-users] pdb2gmx assign CSER to non-terminal serine

Thank you Justin!!! That's the problem. Now everything runs well. Ruan On Tue, May 3, 2016 at 12:04 PM, Justin Lemkul wrote: > > > On 5/3/16 12:02 PM, Zheng Ruan wrote: > >> Hi Gromacs Users, >> >> I'm using pdb2gmx to process my pdb files with a phospho-tyrosine >> using amber99sb-ildn.ff. The

Re: [gmx-users] gmx hbond - specify precise atom names involved

Thanks Justin, I’ll give that a try. I assume this approach would still require the .trr to be converted to a .gro file, and then the customised names ‘search-replaced’ with the respective ‘fake’ names? Thanks Anthony On 03/05/2016 16:22, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on be

Re: [gmx-users] gmx hbond - specify precise atom names involved

On 5/3/16 5:21 PM, Nash, Anthony wrote: Thanks Justin, I’ll give that a try. I assume this approach would still require the .trr to be converted to a .gro file, and then the customised names ‘search-replaced’ with the respective ‘fake’ names? No. Names are read from the reference coordina

[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

Hi Gromacs users, I just started to develop a scripting framework for Gromacs, it makes some assumptions about the directory structure and command parameters. You cannot prepare or run two different systems in the same directory and always pass the -deffnm option to mdrun. It is very nice! Its m

Re: [gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

Installation is now working. The upload script was broken. 2016-05-03 21:50 GMT-03:00 Pedro Lacerda : > Hi Gromacs users, > > I just started to develop a scripting framework for Gromacs, it makes some > assumptions about the directory structure and command parameters. You > cannot prepare or run

[gmx-users] Umbrella sampling version 5.0

I have used the older version of Gromacs 4.x.x to do umbrella sampling; I have just installed Gromacs 5.0 and found that the tutorials on line are now for Gromacs 5.1. Is there a huge difference in the protocol from 5.0 to 5.1? I used a youtube illustration to install Gromacs. I tried to install

Re: [gmx-users] Umbrella sampling version 5.0

On 5/3/16 9:18 PM, Steve Seibold wrote: I have used the older version of Gromacs 4.x.x to do umbrella sampling; I have just installed Gromacs 5.0 and found that the tutorials on line are now for Gromacs 5.1. Is there a huge difference in the protocol from 5.0 to 5.1? I used a youtube illustr

[gmx-users] Relative FEP topology question - What to do with state B dummy atoms in the .itp file under [ bonds ], [ angles ] and [ dihedrals ]

Hi Gromacs Users, Just some background - I am doing FEP to determine the difference in binding free energy between two ligands (state A and state B) wherein state A has an isopropyl ether group and state B has a methyl ether group in its place. In other words I am transmuting the isopropyl group

Re: [gmx-users] Relative FEP topology question - What to do with state B dummy atoms in the .itp file under [ bonds ], [ angles ] and [ dihedrals ]

You do not "annihilate" bonded terms, otherwise you end up with an atom gas in end state (see the Boresch papers from 1999). You keep those bonds intact, easiest to keep those the same as the initial state so no B state column. We had a discussion about this here just a few months ago. ___