[gmx-users] (no subject)

Thanks a lot！ In fact, I just can not confirm the value of pconc or nconc of the polar.mdp, namely under what conditions should I set “0” or “0.150”？ *Yours sincerely* *Yujie, liu* -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] pulling of a molecule through protein-membrane system

Dear Justin, Well, Charmm-gui not providing an option to make a long box in one direction. So is it fine increasing the box and adding the water in Charmm-gui output pdb file and proceed? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] ligand topology

http://webapps.ccpn.ac.uk/acpype/ On 1 August 2017 at 22:18, Mohammad Zahidul Hossain Khan < za.par...@gmail.com> wrote: > Dear Sir > > I have just use acpype.py -i OAI.pdb > I am getting the error: > ERROR: no 'antechamber' executable! > ERROR: no 'antechamber' executable... aborting ! > ==>

Re: [gmx-users] gromacs rerun calculate the energy

Dear Justin, To get an estimate of the long range interactions in LIE calculations for protein-ligand binding energy calculations, is it reasonable to change the coulomb type to reaction-field zero instead of changing the rcoulomb from 1.0 nanometre to half of the water box, and the

Re: [gmx-users] ligand topology

Dear Sir I have just use acpype.py -i OAI.pdb I am getting the error: ERROR: no 'antechamber' executable! ERROR: no 'antechamber' executable... aborting ! ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set? ==> HINT2: is 'antechamber' in your $PATH? What 'which antechamber' in

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

On 8/1/17 6:07 PM, Ali Ahmed wrote: Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support.

[gmx-users] Doubt about hessian matrix in Normal mode analysis

Dear Justin, I used the following command to print ascii format of the hessian matrix to a file from the default mtx format of gromacs obtained after normal mode analysis. gmxdump_d -mtx nm.mtx > hessian_matrix.dat I would like to confirm the way the hessian matrix is written in this new ascii

[gmx-users] Umbrella Sampling with Direction-Periodic

Hello, I am using a pull code with geometry=direction-periodic and attempting to use gmx wham to construct the free energy. The pulling code is doing what I would like it to, but as might be expected from direction-periodic, when the pull distance is more than half the box length the distance is

Re: [gmx-users] gromacs rerun calculate the energy

Hi, You can't get an estimate including the long-range interaction by using a short-ranged method. If the long range matters, it'll be wrong and if it doesn't, you won't know that. Mark On Tue, 1 Aug 2017 22:43 Varvdekar Bhagyesh Rajendra < bhagyesh.varvde...@research.iiit.ac.in> wrote: > Dear

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Dear Dr. Dallas, Thank you for your reply. Actually, I'm new to GROMACS and I appreciate your support. -- Here is what I get

[gmx-users] Doubt about hessian matrix in Normal mode analysis

Dear all, I used the following command to print ascii format of the hessian matrix to a file from the default mtx format of gromacs obtained after normal mode analysis. gmxdump_d -mtx nm.mtx > hessian_matrix.dat I would like to confirm the way the hessian matrix is written in this new ascii

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Copy the output from both of those commands, most importantly (as Mark has asked) that from the first one gmx grompp You need to show people exactly what you are seeing, not what you say you are seeing. The latter you are filtering it, and most likely not providing all the important information.

Re: [gmx-users] ligand topology

I have found However, if one wants *acpype* just to emulate *amb2gmx.pl*, one needs nothing at all but *[http://www.python.org Python]*. At the moment, *acpype* is only available for download via *svn*: * `svn checkout http://acpype.googlecode.com/svn/trunk/ acpype` Yet, if some reason you

[gmx-users] Doubt about hessian matrix in Normal mode analysis

Dear all, I used the following command to print ascii format of the hessian matrix to a file from the default mtx format of gromacs obtained after normal mode analysis. gmxdump_d -mtx nm.mtx > hessian_matrix.dat I would like to confirm the way the hessian matrix is written in this new ascii

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Dear Mark Yes, all the warnings are from grompp. I have no idea where is the problem in the structure or the topology Thank you On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham wrote: > Hi, > > Did you get any warnings from grompp? > > Mark > > On Mon, Jul 31, 2017 at

Re: [gmx-users] ligand topology

Actually, GAFF forcefield and amber forcefields are compatible. gaff is simply amber ff for small molecules. You have to get first amber tools. The last release is amber tools 16 Get the source code from here : http://ambermd.org/AmberTools16-get.html after installation you can use antechamber

[gmx-users] pulling of a molecule through protein-membrane system

Dear all gromacs users, I would like to build a protein-membrane system to perform umbrella simulation; I need to calculate the molecule transportation by pulling it from top to bottom. In the tutorial, it says "Some force fields include everything you need. For instance, it is unwise to try to

Re: [gmx-users] Creating Custom .rtp files

please finde the files attached to this email: log-files for the 5.1.2 version and the 2016.3 version, also again the .rtp file and the .pdb file Am 01.08.2017 um 00:48 schrieb Justin Lemkul: On 7/31/17 7:47 AM, Momin Ahmad wrote: Hello, the .rtp file is located in the same directory as

[gmx-users] pme algorithm

Hi all, I used Gromacs run the biological system, which contains water, ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype was PME and the cutoff was 10 angstrom, then I want to use the commond rerun to calculate the interaction of resid 1 and resid 2, I add

Re: [gmx-users] Some problem about the process of calculating MM-PBSA binding free energy

Thanks a lot！ In fact, I just can not confirm the value of pconc or nconc of the polar.mdp, namely under what conditions should I set “0” or “0.150”？ Yours sincerely Yujie, liu -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)

Dear gromacs users, I have 2 trajectory files as pdb format. I want to have only one file using the following command: gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime I encountered with: --- Command line:

[gmx-users] PCA in dihdral space

Dear Gromacs users! In the tutorial I found that tomake a list for dihedral angles via mk_angndxI need to provide tpr file as an input. Here some of my questions: 1)Is itpossible to make a list from pdb file (or convert pdb to tpr),assuming that my trajectory has been calculated not in

Re: [gmx-users] ligand topology

Please this GitHub link is totally outdated and not linked in any sense to the original authors. Get the correct ACPYPE here: svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ stable/ccpn/python/acpype acpype On 1 August 2017 at 15:00, Suhaib Shekfeh

Re: [gmx-users] ligand topology

On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote: Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). GAFF is compatible with AMBER (by design). My comments were warning that one should not use AMBER for

Re: [gmx-users] ligand topology

Dear Sir Thank you very much. On Tue, Aug 1, 2017 at 7:00 AM, Suhaib Shekfeh wrote: > Actually, GAFF forcefield and amber forcefields are compatible. gaff is > simply amber ff for small molecules. > You have to get first amber tools. The last release is amber tools 16 >

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Hi, Thank you for your help. well I used this command gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em and I got all the warnings. Here is my em.mdp - integrator = steep

Re: [gmx-users] ligand topology

Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). Best regards. Lucio Montero. Enviado desde Correo para Windows 10 De: Alan Enviado: martes, 1 de agosto de 2017 11:01 a. m. Para: Gromacs Asunto: Re: [gmx-users]

Re: [gmx-users] Creating Custom .rtp files

On 8/1/17 10:32 AM, Momin Ahmad wrote: please finde the files attached to this email: log-files for the 5.1.2 version and the 2016.3 version, also again the .rtp file and the .pdb file The screen output seems garbled to me, with the fatal error coming before the force field selection, and

Re: [gmx-users] Some problem about the process of calculating MM-PBSA binding free energy

On 01/08/17 04:15, yujie Liu wrote: Dear users; I met some problem when I calculated the binding free energy between protein and ligand by the g_mmpbsa program. I am sure that I had read the tutorials of its official website and some other related information, but I don’t know what should I set

Re: [gmx-users] pulling of a molecule through protein-membrane system

On 8/1/17 10:01 AM, Alex Mathew wrote: Dear all gromacs users, I would like to build a protein-membrane system to perform umbrella simulation; I need to calculate the molecule transportation by pulling it from top to bottom. In the tutorial, it says "Some force fields include everything you