This is nothing to do with the GROMACS software, you should be asking
http://www.swissparam.ch/
The error seems to be self explanatory, did you check your mol2 file?
http://www.swissparam.ch/SwissParam_mol2_file.html
I would suggest loading the mol2 file you have using pymol or vmd, and
check to
Dear Gromacs users,
I am looking to use the a99SB-disp forcefield from Robustelli et al.
PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3.
The details of the forcefield are in the paper supplementary material. I
have carried out the following steps:
- Downloaded the Amber
Hi,
Was -DCMAKE_PREFIX_PATH set to the location at which CommLib library was
installed?
Not sure if
-DCMAKE_INSTALL_PREFIX:PATH=/home/derk/Prog/gmx19
is a typo and should be
-DCMAKE_INSTALL_PREFIX_PATH=/home/derk/Prog/gmx19
prepare-qmmm.py
does not seem to be in the sources at
https://gi
Hello,
After compiling GROMACS with the MiMiC option, I was not able to locate the
prepare-qmmm.py file. I do not know whether this is a result of a faulty
installation or if it is something else
I used the following flags:
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_DOUBLE=ON -
Hi Yeping,
A full build may be helpful to run the initial correctness tests, once
you have done this can then use -DGMX_BUILD_MDRUN_ONLY=on for production
runs. Having a full version of GROMACS on a node with access to the same
file system where you do runs is also helpful since there may be
Hi Benson,
I feel I may need to add the following options to cmake?
-DGMX_MPI=on
-DGMX_SIMD=xxx
-DGMX_BUILD_MDRUN_ONLY=on
Should I?
--
From:孙业平
Sent At:2019 Jun. 30 (Sun.) 08:36
To:gromacs ; Benson Muite
Subject:Re: [gmx-users] Ho
Dear all,
I have been trying to use gmx gangle for the calculation of the following
angle :
I have a group of 3 residues and another group of 4 residues. I want to
define a vector which goes through the center of mass of these two groups
and I am interested in calculating the angle of the vector
Dear Gromacs Users,
I'm simulating an ionic liquid with AMBER 99sb-ildn ff in GROMACS 5.1.4
package. With charges +1 and -1 on the cation and anion respectively, the
system is neutral and the minimization is okay. But on scaling the charges
by 0.8, the total charge shows to be above 6000, for a sys
Dear GROMACS users and developers,
I want to run MD simulation of a protein bound to FAD using CHARMM36 force
field. However, I need to generate the parameter files of FAD first.
Hence, I followed the following steps:
1. Downloaded the .pdb structure file from RCSB PDB databank
2. Kept