to be substituted by -SH
group to form a disulphur bond. So, Is there any one who can teach me how to
get a topology file of a protein like this?
Thank you in advance.
Best
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
No.826 Zhang Heng Rd. Shanghai, China, 200032
Tel
Hello, Justin
As the mannul said, it is intended to analyze .pdo files generated by mdrun
using
umbrella sampling tocreate a potential of mean force (PMF). But i were using
AFM method not umbrella sampling. How can i do that? Thanks.
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Hello everybody,
I have recently run a SMD with AFM method, and i got the .pdo file. But i
don't know how to use the .pdo file to calculate the PMF profile. Could
someone give me some suggestion? Thanks a lot.
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi
Hi,
You should include the topology file of DMPC in your current directory. The
present version of Gromacs seems not include the DMPC in their database.
Good luck
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
Shanghai
Date: Thu, 19 Mar 2009 13:52:09 +0800
From: huifang liu huifangliu1...@gmail.com
Subject: [gmx-users] how to get the the force plot after pulling
dynamic simulation using GMX-3.3
To: gmx-users@gromacs.org
Message-ID:
e523c6be0903182252i114666bam4bbe591a10a30
I am recently doing a SMD. I think i did it very well. But i don't know how
to get the force plot. Is there some one can give me a suggestion?
Thank you very much.
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O
Hello gmx-users,
I find the pulling direction in PULL INFO section of the log file is not
coincident with the afm_dir1 parameter i defined in the pull.ppa. could some
one tell me which direction is actually used in the pulling process?
Thank you very much.
Huifang Liu
--
Huifang Liu (Ph.D
options of
afm_dir1 and afm_init1?
Thank you very much!
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264
attention. Hope for your reply
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264
?
By the way, I am sorry that i made a mistake. My workstation has two 4-cords
CPU, not two 8-cords CPU.
Huifang.
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail
= : 104
In addition, it runs very well, when i use '-np 5'
Hope for your help. Thanks
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1
Hi, gmx-users
i want to use gromacs to pull a small ligand through a protein channel and
study the interaction between the ligand and the protein during this
process. However, i have not found out any useful information about steered
molecular dynamics(SMD) using Gromacs software.
What are the
Hi, Gromacs users,
This command grompp_ompi -np 6 -f pr_10_200.mdp -c
after_em_newton_1000.gro -p all.top -o pr_10_100.tpr -po
mdrun_pr_10_100.mdp run normally. But when i run the next command mpirun
-np 6 mdrun_ompi -s pr_10_100.tpr -c after_pr_10_100.gro -o
after_pr_10_100.trr -e
Hi, Gromacs users,
I was caught by a big problem with molecular dynamic investigation of an
cyclic peptide nanotube. When i do energy minimization with em.mdp parameter
file as follows, it gave out a warning: Warning: 1-4 interaction between 135
and 144 at distance larger than 1 nm. I ignored it
I typed this command: grompp -f em.mdp -c speptide.pdb -p
\#spetide.top.1#\ -o speptide_em.tpr
It responded to me like this:Invalid command line argument:
speptide_empdb.tpr
I am a new -learner.Can you tell me where the problem is.
Thanks.
___
Hi,
I am a new learner of Gromacs.I want to kown what relationship between the
spetide.gro file and the #spetide.gro.1# file is and how to see the content
of the #spetide.gro.1# file.
Hope to get your help!
___
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