Date: Fri, 2 Jun 2017 10:57:33 +0000
Hi Hannes, Thanks for your email. This is how I have done: cpptraj -p *.parm7 >trajin *.nc 100 100 1 >strip :WAT,Cl- >trajout *.pdb pdb >run Please see the attached image for reference. Coloured in yellow is suppose to be bonded (-SS-) and the one in red is unbonded (-SH SH-). while preparing the input files for simulation I have specifically mentioned 'bond mol.4.SG mol.30.SG'. I still see it unbonded (marked in yellow). this is how my tleap file reads: source leaprc.protein.ff14SB source leaprc.water.tip3p source leaprc.gaff mol = loadpdb with_ss.pdb bond mol.4.SG mol.30.SG bond mol.15.SG mol.37.SG bond mol.19.SG mol.39.SG mol1 = loadpdb without_ss.pdb bond mol1.15.SG mol1.37.SG bond mol1.19.SG mol1.39.SG protein = combine {mol mol1} solvateOct protein TIP3PBOX 12.0 saveamberparm protein protein.parm7 protein.rst7 After this, I run tiMerge to remove duplicates. Am I doing something wrong?Kindly, suggest me. ________________________________________ From: Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk] Sent: Friday, June 02, 2017 12:35 PM To: amber.ambermd.org Subject: Re: [AMBER] TI MD simulation Your problem doesn't seem to be related to simulation but rather to how you extract structures from the trajectory(?). You only say that "it does not seem to work" without giving any details as to what you have actually done e.g. what software/procedure you have been using and what the result was. Cpptraj should be able to extract coordinates based on a user supplied mask. On Fri, 2 Jun 2017 10:24:48 +0000 Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote: > Dear All, > I have run a short TI simulation on a system using pmemd wherein, I > have in one state bonded disulphide bridge (state A) and in the other > unbonded bridge (State B). > > The peptide I am working with is 40 residues long. > > In my simulation, I have > timask1 = ':4,30', > timask2 = ':41,42', > > when I extract pdb from a certain frame. I wish to make two distinct > PDB for the two states. > > When I replace the coordinates of residue 41, 42 with 4 and 30 > respectively to get PDB of just the state B, it does not seem to work. > > Can somebody kindly suggest me how do I extract pdb of the two states? > > Thanks > Regards > Sowmya > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/png attachment: Screenshot_from_2017-06-02_12-46-42.png)
