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Questions related from Sourav Pal
We have placed a dimer protein into gromacs energy minimization utilising OPLS force fields. but after running 9567 its get minimized. But the problem is that after energy minimization one gap...
12 December 2018 8,885 4 View
I want to perform a protein-DNA-ligand complex simulation by gromacs. but my system contain two ligands named PTR and LIG. but when ever i am going to perform the energy minimization. This is...
12 December 2018 4,686 2 View
hello, I want to do gromacs simulation of a protein DNA complex along with a small molecule ligand. But unfortunately the bound ligand is not a complete one..its one helix is cut. So, i am...
12 December 2018 3,842 6 View
I have a trimeric protein which have a lots of missing residues. that why i decided to build homology modelling. but after successfully modelling each chain contains maximum loop like structure...
04 April 2018 8,352 5 View
I have a protein containg 2138 amino acids in each chains. then i added POPC membrane and then add solvent ater and counter kcl ions..then i had done 025ns run for eqilibration by restrating...
09 September 2017 3,131 5 View
Hello Everyone, I have a AUTODOCK docking PDB file for both Protein-Ligand-DNA Complex. I want to do simulation of these complex. but simulation failed due to unrecognized ATOM TYPES present into...
06 June 2017 5,400 5 View
I asked you a question about some problems regarding the ACPYPE error. I installed the ACPYPE according the https://code.google.com/archive/p/acpype/wikis/TutorialAcpype4Gromacs.wiki.but when I...
06 June 2017 6,649 0 View
actually i am new in gromacs, i started to follow the protein ligand simulation tutorial from gromacs server, but there i cant understand how will i make the topologies from PRODRG webserver. can...
06 June 2017 7,707 15 View
i have 3 chains protein. but i want to open this chains by applying pulling force on the proteins. can you please suggest me what will be TCL Scripts.
12 December 2016 4,532 1 View
we didn't find any specific TLR7 specific antagonist . maximum are dual antagonist of TLR7 and TLR9 antagonist. Is there any specificity on the protein active site? what was the reason for that?
09 September 2016 8,584 6 View
i want to perform steered molecular dynamics on a channel protein for opening up their gating pathway. for that reason i want to apply a force on multiple atom (E.g minimum 2 amino acid...
08 August 2016 7,278 3 View
I am doing SMD of protein using NAMD with constant velocity pulling. In order to do the simulation, we have to specify the smd-atom (the atom to which the dummy atom is attached and then pulled)....
08 August 2016 6,695 2 View
i actually made a water sphere of a protein but after making this, it will not be proper sphere shape in namd. and some of the water molecule in pdb file is un numbered . here i have attach the...
07 July 2016 7,842 3 View
please give me a suggestions. i have a trans membrane proteins with 3 chains.
07 July 2016 5,583 9 View
i made a thickness of transmembrane of 100 * 100 on vmd. but can we reduce the thickness of the transmembrane on vmd ?
07 July 2016 3,261 7 View
