Re: [gmx-users] genbox error at futil.c
iulek wrote:
Thanks for replying.
Humm..., maybe I see now. As a beginner I intended to keep all files
produced and better inspect what happens in sequence, but I did not want
to use the conventional renaming. But it seems that for the topology
file, the common procedure is to keep always one only name through the
several steps, right? That is what I understand with
You can keep the same name, or manually make your own backup copies along the
way (topol_orig.top, topol_after_sol.top, etc).
"
Option Filename Type Description
-p topol.top In/Out, Opt. Topology file
"
so, the same name for input and output, yet genbox renames the old
one according to the conventions (which in my script I could then
further "re-rename").
Right, genbox will not make a new file for you, it simply processes the input
topology, which becomes the output once it is modified.
-Justin
And... genbox does need a previous topology file (RecA_nat_b4em.top
was intended to be the output file!).
Thanks, again.
Jorge
iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein
in a water box, after doing some (web) tutorials. I googled first for
this (possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
"
Processing topology
---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
---
"
So is the topology in the current working directory?
-Justin
The command line is:
> genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro << eof > genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Re: Re: [gmx-users] genbox error at futil.c
Thanks for replying.
Humm..., maybe I see now. As a beginner I intended to keep all files
produced and better inspect what happens in sequence, but I did not want
to use the conventional renaming. But it seems that for the topology
file, the common procedure is to keep always one only name through the
several steps, right? That is what I understand with
"
Option Filename Type Description
-p topol.top In/Out, Opt. Topology file
"
so, the same name for input and output, yet genbox renames the old
one according to the conventions (which in my script I could then
further "re-rename").
And... genbox does need a previous topology file (RecA_nat_b4em.top
was intended to be the output file!).
Thanks, again.
Jorge
iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein
in a water box, after doing some (web) tutorials. I googled first for
this (possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
"
Processing topology
---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
---
"
So is the topology in the current working directory?
-Justin
The command line is:
> genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro << eof > genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
___
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Re: [gmx-users] genbox error at futil.c
iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein in a
water box, after doing some (web) tutorials. I googled first for this
(possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
"
Processing topology
---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
---
"
So is the topology in the current working directory?
-Justin
The command line is:
> genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro << eof > genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
___
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] genbox error at futil.c
Hi!
I am a very beginner, trying to make some dynamics of a protein in
a water box, after doing some (web) tutorials. I googled first for this
(possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
"
Processing topology
---
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
---
"
The command line is:
> genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro << eof > genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
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