Re: [GaMD-discuss] Question about proper sigma0P value
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Re: [GaMD-discuss] Question about proper sigma0P value
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From: Xiao, F. <Fu...@me...> - 2025-07-19 00:25:32
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Hi Qianwei, I think the parameters of "timask1" and "scmask1" in your input file are a bit strange. These two parameters are the sequence numbers of the ligand in the amber format protein complex (pdb4amber command line can do this). Similar to the red box marked in the following picture (BEN is a small molecule). [cid:bc75a470-c323-4303-88c7-ed6455b0cb77] Small molecules are represented by an integer number, while peptides/antibodies are indicated by a sequence number such as xxx-xxx. In addition, iE = 2 can be deleted. Maybe you can try to check your parameters carefully. Best, Fu Xiao ________________________________ From: Miao, Yinglong <Yin...@me...> Sent: Friday, July 18, 2025 17:05 To: Li, Joyce <JO...@pi...> Cc: gamd-discuss <gam...@li...>; Xiao, Fu <Fu...@me...>; Joshi, Keya <ke...@em...> Subject: Re: [GaMD-discuss] Question about proper sigma0P value Hi Qianwei, I’m CC’ing Fu and Keya, experts in LiGaMD3 in our lab, and they may be able to help you more. Best, Yinglong Yinglong Miao, Ph.D. Associate Professor Department of Pharmacology and Computational Medicine Program University of North Carolina - Chapel Hill Tel: 1-919-962-5696 http://miaolab.org Editor-in-Chief npj Drug Discovery https://www.nature.com/npjdrugdiscov On Jul 17, 2025, at 6:36 PM, Li, Joyce via GaMD-discuss <gam...@li...> wrote: Hello, I am trying to use LiGAMD3 for measuring the binding kinetics between protein and ligand. The system I use is PDB 5JID. The original system has two ligands, but I kept only one for the GAMD. I followed the discussions in paper (10.1021/acs.jctc.4c00502) and tried to find the right sigma0p for unbinding the ligand. But even if I set the sigma0P to 8, the ligand still binds with the protein and the ligand RMSD is lower than 2 A after 100 ns production run. Attached are the codes for the simulation (pasted below as well) and the log file for the 100 ns production when P is 8. Did I do something wrong, or should I go for an even much higher P value? I have been trying this for months but not seenthe ligand to move. So I will appreciate any suggestions! Thank you, Best, Qianwei equbrilium cMD and GaMD equilbrium &cntrl ig = -1, ! Pseudo-random number generator (random seed based on time) ntx = 1, ! no initial coordinates and velocity(ASCII) imin = 0, ! Minimization (No) irest = 0, ! Restart the Simulation? (no) use previous velocity cut = 8, ! Non-bonding Cut-off (8 A) ntc = 2, ! SHAKE bond length constraints (constrain bonds with H) ntf = 1, ! compelete interaction is calculated tol = 0.000001, !relatve geometrical tolerance in shake dt = 0.002, ! timestep = 2fs iwrap = 1, !set for long runs to keep coordinate from overflowing nstlim = 44000000, ! Simulation length (sum of ntcmd and nteb total 88 ns) ntb = 2, ! PBC (Constant pressure) ntp = 1, ! isotropic position scaling barostat = 1, ! for control pressure, Berendsen ntt = 3, ! Temperature scaling (Stochastic version of Berendsen thermostat) gamma_ln=5.0, temp0 = 300, ! Reference temperature (300K, physiological temperature) tempi = 300.0, !Initial temperature ntpr = 500000, ! Energy save interval (every 500000 steps or 1 ns) ntwx = 500000, ! Coordinate/trajectory save interval (every 500000 steps or 1 ns) ntwprt = 7101, !number of atoms to be saved ntwr = 5000000, ! Write restart file every 10 ns igamd = 28, iE = 2, !thershold energy to the lower bound irest_gamd = 0, !not a restart gamd ntcmd = 4000000, !8 ns cMD nteb = 40000000, !80 ns GAMD ntave = 400000, !four times total number of atoms ntcmdprep = 800000, !1.6 ns number of cMD not collected for statistics calculation ntebprep = 800000, !1.6 ns GAMD for preperation sigma0P = 8.0, sigma0D = 6.0, sigma0B = 6.0, iEP=2, iED=2, iEB=1, bgpro2atm=1, edpro2atm=7076, gti_cpu_output=0, gti_add_sc=1, icfe = 1, ifsc = 1, timask1=':7077-7101', scmask1=':7077-7101', timask2='', scmask2='', &end END production GaMD production &cntrl ig = -1, ! Pseudo-random number generator (random seed based on time) ntx = 1, ! no initial coordinates and velocity(ASCII) imin = 0, ! Minimization (No) irest = 0, ! Restart the Simulation? (no) use previous velocity cut = 8, ! Non-bonding Cut-off (8 A) ntc = 2, ! SHAKE bond length constraints (constrain bonds with H) ntf = 1, ! compelete interaction is calculated tol = 0.000001, !relatve geometrical tolerance in shake dt = 0.002, ! timestep = 2fs iwrap = 1, !set for long runs to keep coordinate from overflowing nstlim = 50000000, ! Simulation length (sum of ntcmd and nteb total 100 ns) ntb = 2, ! PBC (Constant pressure) ntp = 1, ! isotropic position scaling barostat = 1, ! for control pressure, Berendsen ntt = 3, ! Temperature scaling (Stochastic version of Berendsen thermostat) gamma_ln=5.0, temp0 = 300, ! Reference temperature (300K, physiological temperature) tempi = 300.0, !Initial temperature ntpr = 250000, ! Energy save interval (every 250000 steps or 500ps) ntwx = 500, ! Coordinate/trajectory save interval (every 500 steps or 1ps) ntwprt = 7101, !number of atoms to be saved ntwr = 5000000, ! Write restart file every 10 ns igamd = 28, iE = 2, !thershold energy to the lower bound irest_gamd = 1, !a restart gamd ntcmd = 0, !no cMD nteb = 0, !0 GAMD ntave = 400000, !four times total number of atoms ntcmdprep = 0, !no cMD preperation ntebprep = 0, !noGAMD for preperation sigma0P = 8.0, sigma0D = 6.0, sigma0B = 6.0, iEP=2, iED=2, iEB=1, bgpro2atm=1, edpro2atm=7076, gti_cpu_output=0, gti_add_sc=1, icfe = 1, ifsc = 1, timask1=':7077-7101', scmask1=':7077-7101', timask2='', scmask2='', &end END _______________________________________________ GaMD-discuss mailing list GaM...@li...<mailto:GaM...@li...> https://lists.sourceforge.net/lists/listinfo/gamd-discuss |
