Gromacsers
I have been running jobs successfully for a while, submitting them directly,
but when I submitt them to the q (qsub) I get an error from grompp that it
can't find "libXm.so.3". I recompiled with configure option
--without-motif-include, but that did not get rid of the problem. How
Mark
I'm sorry--that is not what I was saying at all--I did not have ANY waters
originally defined in my .top file. I used editconf to make a cubic box that
was 6 x 6 x 6 , then used genbox and in that step specified which topology file
in which to insert the waters--a .top file with no water.
Dear gromacs guys
Why would genbox put more water molecules in my .gro file than in my .top file?
I'm sure all I have to do is edit the number in my top file, but I have not had
this happen before, does anyone know of a reason that this happens so I can
fix my file?
Will Welch
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Nevermind, I made one using VMD, it solvated my protien just fine.
- Original Message -
From: WILLIAM R WELCH <[EMAIL PROTECTED]>
Date: Friday, February 2, 2007 3:25 pm
Subject: [gmx-users] genbox using TIP3P?
To: Discussion list for GROMACS users
> Hello
> I would lik
Hello
I would like to use the TIP3P model in my calculation, and I would like to be
able to use genbox to solvate a pepetide, but there is no TIP3P.gro coordinate
file in the program. I there such a coordinate file available?
Will
- Original Message -
From: [EMAIL PROTECTED]
Date: Frida
The links for "Getting Started-Main Table of Contents" on the
page(www.gromacs.org/blogcategory/page_2.html) are all broken. Does anyone
know of a way to access these files?
Will
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http://www.gromacs.
Hello, I am a brand new gromacs user--I have been banging my head against the
wall with the manual for some time, so if someone could be so gracious, I have
2 simple questions:
In the tutorial files I obtained in gromacs 3.3, on if I use pdb2gmx with no
file specified, I get the input/output er
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