Re: [gmx-users] spatial restraints

Hi Stefano, You may consider "gmx make_ndx" to make an index file and append a restraint section (POSRES) at the end of your existing topology to call the indices. I think this is a minimal alteration to your topology. Regards, Simon 在 2018年6月19日週二 08:17，Stefano Guglielmo 寫道： > Hello gromacs

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

; It is also in the ubuntu repo. > You should to get mkdssp and/or dssp to work on their own and if you can't > then your problem is not with gmx. > > On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu < > simoncks1...@gmail.com > > wrote: > > > Hi everyone, >

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

gt; with the -ver option." > > Did you follow the error message suggestion? With DSSP 2.2.1 you need to > set "-ver 2" on your gmx do_dssp command. > > J > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu < > simoncks1...@gmail.com> > wrote: > &g

[gmx-users] GROMACS 5.1.4 and dssp 2.2.1

Hi everyone. I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned an error: Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. I can run mkdssp and it is placed in bin. Is it a compatibility problem here? Thanks in advance.

Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

Hi everyone, Our group is also interested in purchasing cloud GPU cluster. Amazon only supplies GPU cluster connected by 10Gb/s bandwidth. I notice this post but there is no reply by far. It would be nice if someone give any clue. Regards, Simon 2018-03-06 1:31 GMT+08:00 Daniel Bauer

[gmx-users] modifying aminoacids.n.tdb in amber14sb.ff

Hi everyone, I am trying to add new terminal capping as VAL-NH2 in amber14sb.ff/aminoacids.n.tdb. I refer to charmm36-nov2016 and created my VAL-NH2 without caring about the charges first. Meanwhile, aminoacid.rtp remains the same. *aminoacids.n.tdb* ; manually added VALN ( VAL neutral - NH2

Re: [gmx-users] Choosing terminals with AMBER ff

raham" <mark.j.abra...@gmail.com> 寫道： Hi, AMBER didn't parameterize things that likely don't exist under biological conditions. You can build on a proper capping group that is present in aminoacids.trp, however, such as ACE. Mark On Wed, Nov 8, 2017 at 7:24 AM Simon Kit Sang Chu <sim

[gmx-users] Choosing terminals with AMBER ff

Hi everyone, I am considering selecting specific terminal caps, i.e. neutral N-terminal, charged C-terminal, with AMBER forcefield. However, there does not seem such an option. I ran "gmx pdb2gmx -f protein.pdb -o protein.gro -p protein.top -i protein.itp -ter -ignh". After selecting

Re: [gmx-users] No default Proper Dih. types when using neutral terminal

Hi everyone, Last time, I mentioned missing parameter for neutral terminal dihedral and U-B type. After some debugging, I am still not sure what the cause was. I hope providing more information could help to resolve the issue. I am using CHARMM36 forcefield. Brief summary of the problem - No

[gmx-users] No default Proper Dih. types when using neutral terminal

Hi everyone, I have a list of short peptides generated from PyMOL. I am ignoring all the hydrogen atoms and use neutral terminal caps for both ends. All seems fine from pdb2gmx to solvation. The problem kicks in when I add ions. *Here was what I did - * 1. pdb2gmx 2. editconf 3.

[gmx-users] CHARMM36 older version (GROMACS)

Hi everyone, I plan to use CHARMM36-nov2016.ff for my simulation. However, MacKerell Lab webpage does not seem to provide CHARMM36-nov2016. Only CHARMM36-jul2017 is provided. I tried to google "CHARMM36-nov2016" but failed to see any official

[gmx-users] nstcomm < nstcalenergy

Dear every user, I am using Andersen thermostat and nstcomm should be set to 1 (step). However, after specifying nstcomm = 1, an error has returned - nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it to nstcalenergy step. I fail to search for "nstcalenergy" in neither

[gmx-users] Andersen thermostat with NPT - nstcomm < nstcalenergy

Hi every user and supporting staff, I am using Andersen thermostat in NPT simulation. nstcomm was required to be 1. However, I received another complaint - nstcomm < nstcalenergy. Yet, I failed to find nstcalenergy in neither mdp and manual. Is there anywhere I missed to calibrate nstcalenergy?

[gmx-users] distance restraint in gromacs md run

Hi, I have a protein of interest which requires distance restraint for C alpha atoms. However, the simulation does not seem to include the restraint at all. *prod.mdp* define = -DPOSRES constraints = none integrator = md dt = 0.005 nsteps

[gmx-users] Lenard Jones interaction between two chains

Hi, I am working on a protein dimer. Since they are not linked by a bond, after pdb2gmx two topology files are produced. Each of them contains all atoms in their individual chains and their respective posre.itp contains information of position restraint. However, after looking into the topology

[gmx-users] Reference point of position restraint

Hi, Just a short question. When I check GROMACS manual, it is stated that position restraint is applying a strong harmonic potential to the atom in reference to a reference point. However, should I assume the reference point is the position of the atom in the first frame? Thanks, Simon --

Re: [gmx-users] number of coordinates does not match after POSRES

> On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote: > >> Hi Mark, >> >> Thanks for your prompt reply. What surprises me is that a change of >> "define >> = POSRES" could cause a problem. The full output from grompp is - >> >> checking inp

Re: [gmx-users] number of coordinates does not match after POSRES

19:18 GMT+08:00 Simon Kit Sang Chu <simoncks1...@gmail.com>: > Hi Mark, > > Thanks for your prompt reply. What surprises me is that a change of > "define = POSRES" could cause a problem. The full output from grompp is - > > checking input for internal consiste

[gmx-users] number of coordinates does not match after POSRES

Hi, Initially, my topology file can run grompp with .mdp and .gro. However, after putting POSRES in my mdp, the warning "number of coordinates does not match" and there is no coordinate recognized in my topology file anymore. Therefore, the option POSRES somehow changes everything. The topology

Re: [gmx-users] forcefield parameter missing

ore clue. Regards, Simon 2017-05-15 17:42 GMT+08:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > It's hard to tell from this fragment. Are your include files all what you > think they are? Does grompp terminal output all make sense? > > Mark > > On Mon, May 15, 201

[gmx-users] forcefield parameter missing

Hi everyone, I need to add a new residue in my forcefield and borrow the atoms and parameter from another existing residue. I encounter missing parameter warning for a number of bonds. However, if I check in .itp, the parameters exist. Is there something I missed? Here is an example I encounter.

Re: [gmx-users] New residue for custom capping

n-specific termini are appropriate. > > From the link I provided: "Add your residue to residuetypes.dat with the > appropriate specification (Protein, DNA, Ion, etc)." > > Mark > > On Fri, May 12, 2017 at 9:39 AM Simon Kit Sang Chu <simoncks1...@gmail.com > > > wrote:

Re: [gmx-users] New residue for custom capping

bra...@gmail.com>: > Hi, > > I suspect you need to add your residue to the class of Protein residues, > per > http://www.gromacs.org/Documentation/How-tos/Adding_ > a_Residue_to_a_Force_Field > > Mark > > On Fri, May 12, 2017 at 9:05 AM Simon Kit Sang Chu <simon

[gmx-users] New residue for custom capping

Hi everyone, I am using a new forcefield which does not give proper neutral capping, but requires me to create a custom made residue for that purpose. Specifically, I want a NH2 cap instead of NH+. I rename VAL1 into VAT1, update .hdb & .rtp. However, when I pdb2gmx -ter to create a topology

[gmx-users] GROMACS3.3.1 - configure: error: invalid variable name: –-with-fft

Hi everyone, Due to some technical issues, I have to install gromacs 3.3.1 in order to incorporate my desired forcefield. Following the instructions, I have to switch the FFT library to fftpack. However, I run into this error whenever I choose the option --with-fft, regardless the library chosen.

Re: [gmx-users] forcefield installation on GROMACS 5.1.4

ACE1.5.itp to *forcefield.itp* instead of aminoacids.itp. Regards, Simon 2017-03-28 0:54 GMT+08:00 Justin Lemkul <jalem...@vt.edu>: > > > On 3/27/17 7:44 AM, Simon Kit Sang Chu wrote: > >> Hi everyone, >> >> Recently I am looking into PACE >> <htt

[gmx-users] forcefield installation on GROMACS 5.1.4

Hi everyone, Recently I am looking into PACE for my system and installation of forcefield is required. The files located inside the forcefield directory is given by - aminoacids.rtp cgWater.itp ffPACE_1.3-c.tdb ffPACE_1.3.hdb ffPACE_1.3-n.tdb