Francesco Pietra wrote:
On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Francesco Pietra wrote:
Thanks, and beg pardon for the pedestrian mistake.
However, I am not yet out. .tpr not generated
With command
$ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o
mod21.cg.tpr
There are: 0 OTHER residues
There are: 1270 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/readir.c, line: 798
Fatal error:
Group DPPC not found in indexfile.
Maybe you have non-default groups in your mdp file, while not using
the '-n' option of grompp.
In that case use the '-n' option.
As I said before, I am using the mdp file as provided by MARTINI.
============
Then you haven't yet appropriately #included the .itp file for DPPC.
As I said, I don't understand why about DPPC. The protein is pure
standard amino acids and nothing else. I am trying to get the files
for simulation in vacuum. I have reexamined all the stuff and I don't
see any allusion to a bilayer, unless that comes from the .mdp file.
The .top I used in these last attempts reads:
I would suggest looking at the .mdp file; grompp wouldn't be complaining if
there wasn't some input file specifying an unknown molecule.
-Justin
;
; mod21 | MARTINI 2.1
;
; Include force field poarameters containing all particle definitions,
; the interaction matrix, plus the topology for water.
#include "martini_v2.1.itp"
; Then include the file(s) containing the topologies of other
; molecules present in your system.
; #include "martini_v2.0_lipids.itp"
; #include "martini_v2.0_salt.itp"
#include "mod21.itp"
; Define a name for your system
[ system ]
mod21
; Define the composition of your system
; The molecule names should correspond to those defined in the itp file(s).
[ molecules ]
Protein 1
; DPPC 128
; W 2000
; NA+ 20
; CL- 20
It seems that commenting out ";" is placed correctly.
I am sincerely sorry to bother you again.
francesco
With command
$ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n
-o mod21.cg.tpr
NOTE:
System has non-zero total charge: -5.000000e+01
processing coordinates...
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BCQd - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SCAC1 - SC1)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BCP5 - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SCP1 - SC1)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BSP5 - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SSAC1 - SC1)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BCP5 - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SCC3 - SC1)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SCQd - SC2)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BCP5 - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SCN0 - SC1)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SCQd - SC2)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BHN0 - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BHNd - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SHAC1 - SC1)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(BHNd - BN0)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SHSC4 - SC2)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SHSP1 - SC1)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SHSC4 - SC3)
Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
(SHSC4 - SC4)
(more than 20 non-matching atom names)
WARNING 2 [file "mod21.cg.top", line 28]:
2875 non-matching atom names
atom names from mod21.cg.top will be used
atom names from mod21.cg.box.gro will be ignored
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# BONDS: 2724
# G96ANGLES: 2860
# PDIHS: 328
# IDIHS: 187
# CONSTR: 745
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/gmxlib/futil.c, line: 345
File input/output error:
index.ndx
==========
Non-matching because of the many -S-S- bonds? Why asking about index.ndx?
Non-matching names occur because MARTINI doesn't assign them correctly in
the initial system setup. Using the .top names is fine.
The I/O error comes from the fact that you have passed the -n flag to grompp
without having index.ndx in the working directory. Note that having an
index file doesn't necessarily solve your problem; the warning is printed in
case you have non-default groups for, e.g., T-coupling or energygrps. If
you have a "moleculetype not found," then you haven't #included the .itp
file and an index file won't save you.
-Justin
Thanks for help
francesco
On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Francesco Pietra wrote:
Hi:
As I found it difficult to manage solvation - the way I would like -
with a pore protein (a trimer) partly immersed into a bilayer, I
started with the protein alone in vacuum, in order to try to fix the
problems step-by-step. Unfortunately, I can't fix simple problems with
grompp.
1) Generated mod21.itp from mod21.pdb
2) Generated mod21.cg.pdb with awk script)
3) editconf -f mod21.cg.pdb -o mod21.cg.gro
4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro
5) grompp -np 4 -f mod21.cg.box.mdp -c mod21.cg.box.gro -p
mod21.cg.box.top -warnmax 10
Error: no such moleculetype Protein.
.............................
.mdp is merely a renamed martini_v2.0.example.mdp, taking care that
"cpp = /usr/bin/cpp".
.top was from editing martini_v2.0.example.top and reads (in between
===):
======
;
; mod21 | MARTINI 2.1
;
; Include force field parameters containing all particle definitions,
; the interaction matrix, plus the topology for water.
#include "martini_v2.1.itp"
; Then include the file(s) containing the topologies of other
; molecules present in your system.
; #include "martini_v2.0_lipids.itp"
; #include "martini_v2.0_salt.itp"
#include mod21.itp
This #include statement has the wrong syntax. See any of the above for
the
correct way to do it.
-Justin
--
========================================
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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--
========================================
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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or send it to gmx-users-requ...@gromacs.org.
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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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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