Hello Dr.Spoel and others,There is one more problem with the simulation of hen egg white lysozyme simulation in water I am running. The timestep I could use is just 0.5 fs or 0.0005ps. Is there any way around to increase the timestep.
This is how a part of my mdp file looks like:; RUN CONTROL PARAM
I will do what you suggest David. But, I have plenty of these lines, so I was
avoiding that method. However, it seems the only solution right now.
Thanks
Murat
> Hi all,
>
> I have a small problem with pdb2gmx. I have a non-standard residue with rtp
> parameters entered manually into oplsaa data
Hello,
I have been having trouble with a topology I created
for androst-5-ene-3,17-dione (GROMOS 96 force field).
I have found the molecule to bend inwards withing 100
ps of equilibration, something which has not been seen
by others who have used CHARMM or AMBER. I have also
tried to convert the t
Hello everyone,
I have been having trouble with a topology I created
for androst-5-ene-3,17-dione (GROMOS 96 force field).
I have found the molecule to bend inwards withing 100
ps of equilibration, something which has not been seen
by others who have used CHARMM or AMBER. I have also
tried to conv
Hi all and Spoel
Based on mailing list answer at Mar 20th 2003, which discribed the
entire topology file for water shell model, referencing on J. Phys.
Chem B. 105 (2618) 2001, I have tryed to run water polarization MD with
this file.itp. However, running grompp a message "Water polarization
shoul
MURAT CETINKAYA wrote:
Hi all,
I have a small problem with pdb2gmx. I have a non-standard residue with rtp
parameters entered manually into oplsaa database. When I try to convert my pdb
file into gro, I get:
-
Program pdb2gmx, VERSION 3.3.1
Source code file: t
Hi all,
I have a small problem with pdb2gmx. I have a non-standard residue with rtp
parameters entered manually into oplsaa database. When I try to convert my pdb
file into gro, I get:
-
Program pdb2gmx, VERSION 3.3.1
Source code file: toputil.c, line: 94
Fatal
Hi Elias,
pdb2gmx does not read CONECT records in the pdb file. You have to add
S(Cys) - Fe bonds in the specbond.dat file. The cause for not getting
any errors is that pdb2gmx sees cysteines, which it can handle, and
iron ions, which it can handle. But it doesn't think of connecting
them and doe
Hi !!
I to construct to the block for residuo FS4 of the two clusters in the .rtp file of the force field ffgmx with all the linkings, angles etc., beyond the on and not on parameters. When I run pdb2gmx, it does not give menssagem of error, but the linkings between the cysteins (SG) and atoms of
Dear DavidThank you for your reply. Your tip it will very usefeul.Bestseef__ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Hi,
On Aug 15, 2006, at 9:49 AM, Berk Hess wrote:
I do not think there is an error in ffG53a6.rtp for TRP.
OPLS and GROMOS use different approaches to keep
rings planar.
I don't know which force field would be closest to reality.
But I think slighlty more or less rigid rings will have little
i
From: Shirley Siu <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] histidine (HISB) planarity >> how about Trp?
Date: Mon, 14 Aug 2006 18:07:13 +0200
Hi everybody,
I am also trying G53a6 in my protein simulation
David van der Spoel wrote:
Samuel Silva Pita wrote:
Dear Mr. Spoel,
i'd described before at GMX lists that my topology of FAD was built by
hand and using the atoms adequately for FF G53a6 at GMX 3.3.1. After
the addition of atoms , bonds, constants ,etc. at ffg53a6.atp,
ffg53a6.hbd and all o
Samuel Silva Pita wrote:
Dear Mr. Spoel,
i'd described before at GMX lists that my topology of FAD was built by hand and using the
atoms adequately for FF G53a6 at GMX 3.3.1. After the addition of atoms , bonds,
constants ,etc. at ffg53a6.atp, ffg53a6.hbd and all others arquives, I proceed to
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