Re: [gmx-users] top parameters for pluronic f127 (Andrian Saputra)

2016-06-05 Thread Andrian Saputra
g_gmx-users digest..." > > > Today's Topics: > >1. Re: top parameters for pluronic f127 (Andrian Saputra) >2. Re: top parameters for pluronic f127 (Andrian Saputra) > > > ------------------ > >

Re: [gmx-users] top parameters for pluronic f127 (Andrian Saputra)

2016-06-05 Thread ABEL Stephane 175950
aputra <andrian.c...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] top parameters for pluronic f127 Message-ID: <calw802k-qyfemakgx52yf5wspxm66s5q9ghtud3m6gmh6r-...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 I have the same problem.. but gasteiger is less a

Re: [gmx-users] top parameters for pluronic f127

2016-06-04 Thread Andrian Saputra
I got the idea... May be you can consider this webpage: webchem.ncbr.muni.cz/Platform/ChargeCalculator#bio-more For efficiently generating charges into large molecules Pada tanggal 5 Jun 2016 10.52, "Andrian Saputra" menulis: > I have the same problem.. but gasteiger is

Re: [gmx-users] top parameters for pluronic f127

2016-06-04 Thread Andrian Saputra
I have the same problem.. but gasteiger is less accurate... anyone can suggest software quickly generating am1bcc, resp, esp charges for big molecules ? Pada tanggal 4 Jun 2016 00.51, "Alan" menulis: > It's too big! It will never work. > > Try the following alternatives: >

Re: [gmx-users] top parameters for pluronic f127

2016-06-03 Thread Alan
It's too big! It will never work. Try the following alternatives: - to use gasteiger charge (and then you get only the topology); - as you said it's a polymer, take the smallest common unit, join 3 pieces of it and get the topology/charges for it, use the middle unit to extend the charge for all

[gmx-users] top parameters for pluronic f127

2016-06-03 Thread SAKO MIRZAIE
-- Forwarded message -- From: SAKO MIRZAIE Date: Fri, 3 Jun 2016 20:04:49 +0430 Subject: top parameters for pluronic f127 To: gromacs.org_gmx-users@maillist.sys.kth.se Dear All, I am trying to convert my mol2 file to amber99sb itp to do MD by gromacs.

[gmx-users] top parameters for pluronic f127

2016-06-03 Thread SAKO MIRZAIE
Dear All, I am trying to convert my mol2 file to amber99sb itp to do MD by gromacs. but, when I use ACPYPE software, it run and never finished. my mol2 file is pluronic F127 and contains 2500 atoms. this structure is a polymer and huge in size. how can I get an itp file for my polymer? How can I

[gmx-users] top parameters for pluronic f127

2016-06-03 Thread SAKO MIRZAIE
Dear All, I am trying to convert my mol2 file to amber99sb itp to do MD by gromacs. but, when I use ACPYPE software, it run and never finished. my mol2 file is pluronic F127 and contains 2500 atoms. this structure is a polymer and huge in size. how can I get an itp file for my polymer? How can I

[gmx-users] top parameters for pluronic f127

2016-06-03 Thread SAKO MIRZAIE
Dear All, I am trying to convert my mol2 file to amber99sb itp to do MD by gromacs. but, when I use ACPYPE software, it run and never finished. my mol2 file is pluronic F127 and contains 2500 atoms. this structure is a polymer and huge in size. how can I get an itp file for my polymer? How can I