Indeed this seems likely. I was able to add 125 urea and solvate w/out
incident doing it in two steps.
Thanks again,
Ken
On Apr 23, 2009, at 1:31 PM, Justin A. Lemkul wrote:
Ken Rotondi wrote:
Dear Justin, All,
Yes, running as two separate steps works, is this a known genbox bug?
I
diala.top
genbox -cp dialaurea.gro -cs spc216.gro -o dialaureasoln.gro -p
diala.top
On Apr 23, 2009, at 12:57 PM, Justin A. Lemkul wrote:
Ken Rotondi wrote:
Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5
Does it work if you use -ci to insert your molecule, then in a
Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5
On Apr 23, 2009, at 11:06 AM, Justin A. Lemkul wrote:
Which version of Gromacs? There was a bug in genbox that was fixed
for version 4.0.4.
-Justin
Ken Rotondi wrote:
Hello All,
I have managed to get urea into the G53a6 ffield
Hello All,
I have managed to get urea into the G53a6 ffield with suitable
adjustments to the appropriate .pdb, .rtp, and .hdb files. I am trying
to use the resulting urea.gro file (I have also tried with a urea.pdb
file generated from the urea.gro file using pdb2gmx) in genbox using
the -
Yes sir, that was the problem
Many thanks,
Ken
On Apr 16, 2009, at 3:33 PM, David van der Spoel wrote:
Ken Rotondi wrote:
Hello all,
I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro
running 10.5. The program configures with out a hitch, but
compiling with the
Hello all,
I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro
running 10.5. The program configures with out a hitch, but compiling
with the make command ends in a recursive error. It seems that it's
not finding something that it should have installed itself, but I
wouldn't
These problems are typically due to grompp not finding cpp (make sure
it's in your path) or having opened the top file in some non-linux
text editor. Open the top file in vi and see if you see 'M^' where
you would expect line breaks. If so your top file is polluted. To
change from mac line
Hi all,
I'm having troubles with grompp.
Building .gro and .top files from a .pdb file of a 7 residue peptide
(61 atoms in uaff) results in a system with 5137 atoms in the gro file
and a .top file with 1 protein (61 atoms) and 1692 solvent (5076
atoms). When I ran grompp it fatal erred stati
I know, enigmatic subject, but it's true.
The program is GROMACS 3.3.1 running on a Fedora linux box. I'm trying
to do the most simple thing, charge balance a system with 1 protein and
solvent. When I try to run grompp to generate a run input file for
genion there is a fatal error stating that
rdware/OS (I'm running on OS X.3.9/G3 and RedHat/P4) run the test.pdb (1 nucleotide) with a .hdb file containing the modifications to see if the problem is reproducible?
On Apr 3, 2006, at 5:26 PM, David Mathog wrote:
Ken Rotondi wrote:
I've had this in AMBER for some time. I need to us
David,
Many thanks, but I've had this in AMBER for some time. I need to use a UAFF.
On Apr 3, 2006, at 1:27 PM, Ken Rotondi wrote:
Hello all,
I added the RNA hydrogens to my ffG53a5.hdb file, which eliminated the H2*, etc. missing from .hdb file errors. However, when I run pdb2gmx on a
Hello all,
I added the RNA hydrogens to my ffG53a5.hdb file, which eliminated the H2*, etc. missing from .hdb file errors. However, when I run pdb2gmx on a test .pdb file with one nucleotide in it returns a fatal error that:
"Atom H211 not found in rtp database in residue GUA, it looks a bit lik
Rob,
Thanks for the clarification. However, the problem is that pdb2gmx does not assign a preprocessor code in the .top file. The .rtp file does have
-O P O5* C5* gd_11
-O P O5* C5* gd_9
for the DNA/RNA backbone, and gd_11 & gd_9 are defined in the .itp file.
Hi All,
I've processed an RNA chain in GROMACS 3.2.1 using the G43a1 ff to .gro and .top files. Upon trying to generate a .tpr file for genion, grompp returned an series of warnings leading to a fatal error, eg.:
WARNING 2 [file "rnatest.top", line 605]:
No default Proper Dih. types, using ze
(sorry about the blank subject in previous post)
Hi All,
I've processed an RNA chain in GROMACS 3.2.1 using the G43a1 ff to .gro and .top files. Upon trying to generate a .tpr file for genion, grompp returned an series of warnings leading to a fatal error, eg.:
WARNING 2 [file "rnatest.top", l
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