Missing values for "intercor" in bestranking.lst output when runing GOLD in parallel with PVM

-
There are some bugs when running GOLD 5.4 in parallel with PVM (parallel virtual machine). In the "intcor", there is not value reported in the final docking result file "bestranking.lst".

Run-1: In parallel with PVM using 8 cpus (parallel_gold_li*)
====================================================
#     Fitness  S(hb_ext) S(vdw_ext)  S(hb_int)    S(int)      intcor     time                               File name                Ligand name
       46.25       9.00       27.86              0.00      -1.06      ----         15.870   './ligands_m1_2.mol2'    'ligand_001'
====================================================

If running GOLD by commond line using "gold_auto gold.conf", this time
gold only used 1 core (cpu), the output file seemed okay as following:

Run-2: Using 1 CPU (gold_linux_64)
====================================================
#     Fitness  S(hb_ext) S(vdw_ext)  S(hb_int)    S(int)      intcor    time                               File name                Ligand name
       46.90       8.99          28.49       0.00           -1.27    -6.29      10.445  './ligand_m1_2.mol2'   'ligand_001'

The CDCC support guy gave the following explanation:

 "Since you are seeing intcor in the output files, this means that you
have the relative_ligand_energy offset set to be on. This option
identifies the lowest value of S(int) from all the GA attempts for a
given ligand and then subtracts that value from the S(int) of each GA
attempt. The resulting value should then be used in the calculation of
the scoring function. You may have uncovered an issue with this intcor
not being reported correctly when running GOLD with PVM, and I will ask
the GOLD developers to look at this.

In the meantime, I would recommend that you use a script to split the
docking of your ligands over different cores, rather than use PVM. We
have such an example script on our website:
http://www.ccdc.cam.ac.uk/support-and-resources/support/case/?caseid=b40a45cb-d4a3-4da3-ae72-b7653398895c
Since you have found that a single, non parallel job is successful, this
should similarly be successful and indicate the intcor value correctly."

 Thus it is not recommended to use GOLD 5.4 with PVM scheduler. However, when using virtual screening setting, comparing the Single-CPU gold runs with PVM gold runs, gives similar results.
Single CPU two repeat runs

Comparing Single-CPU run with PVM parallel run

The fittness scores are not consistent for repeat runs, however, it seems like PVM run gives comparable result as Single-CPU run.

Therefore, it could be no problem to run GOLD docking simulations with PVM parallel run. 

Comments

Post a Comment

Popular posts from this blog

A step-by-step tutorial to perform PCA with Gromacs MD trajectory

-
Image
A step-by-step tutorial to perform PCA with Gromacs MD trajectory It is a common practice to perform principal component analysis to explore the transitions and dynamics of macromolecules simulations.   There may exist multiple states in the free energy landscape, so it is important to extract the representative structures from the energy minima in the free energy surface. To generate such a free energy surface, we could define some collective variables (CVs). However, due to the high dimensionality of the simulation trajectory, it is not always straightforward to select several more important CVs. So the problem is how could we find one or two CVs which could describe the slow motions of the system? To this end, PCA-based dimension reduction and projections could partially solve the problem by transforming the original dataset and grasp the largest variance of the system. Although there has been a tool in Gromacs, which perform the PCA using g_covar and g_anaeig. Th
Read more

Fixing bugs in FF14SB port for Gromacs

-
Bugs? The newly released amber14sb made modifications for protein, DNA and RNA. This force field could be ported into gromacs as I already introduced previous. However, there are some small bugs in the improper dihedral angles of HID, HIE and HIP. So when generating tpr file, errors would be prompted. When run grompp -f npt.mdp -p topol.top -c protein.gro -o product.tpr -n index, errors occur: ERROR 1 [file topolff14sb_Protein_chain_B.itp, line 208041]:   No default Improper Dih. types The reason is that the parameters for some dihedral angles are missing. So we need to fix this. How to fix? Add the following two lines in the ffbonded.itp after the 730th lines: NA  CW  CC  CT       4      180.00     4.60240     2     ;;; HID force field added NA  CV  CC  CT       4      180.00     4.60240     2     ;;; HID force field added The atom type CV and CW here are similar and share the same parameter value. Save the file and run the command again, in general, errors won&
Read more

Install new amber force fields ports in Gromacs

-
Image
Amber force fields are popular for protein, DNA, RNA and lipid simulations. Recently updated amberff12, amberff14 and amberff15 were reported to perform better than amber99sb and amber99sb-ildn. Gromacs is a commonly used simulation software, which using OpenMM to enable GPU acceleration. Gromacs is fast and easy to use. A lot of people use amberff in Gromacs. So to use the newly release amberff12 and amber14sb in gromacs, we need to some work. Step 1. Install Gromacs 4.6.x or Gromacs 5.0.x or Gromacs 5.1.x Installation instructions could be find here: For 4.6.x http://www.gromacs.org/Documentation/Installation_Instructions_4.6 For 5.0.x and 5.1.x http://www.gromacs.org/Documentation/Installation_Instructions_5.0 Suppose you are user john, you installed a gromacs 4.6.7 in /home/john/applications/. After installation, you should source the GMXRC by: source  /home/john/applications/gromacs.4.6.7/GMXRC And add topology files to environments by: export GMXLIB=/home/john/ap
Read more