[gmx-users] Re: +AFs-gmx-users+AF0- Fatal error: number of coordinate file +ADw-cm5+AF8-b4ion.gro, 28016+AD4- does not match

Marco Möller moeller at mail.uni-mainz.de
Wed Mar 23 19:05:16 CET 2005


You might also want to check, that You do not generate Your +ACI-em.mdp+ACI- - 
file with an text editor at a Microsoft Windows System and using it at a 
Unix System for calculations? We have had this topic here before, and 
this hint from an user solved my problems sounding like Yours: the 
Windows text editors usally create CR +- LF at the end of every line, but 
Unix systems expect it to be only LF. There is an open-source editor 
called +ACI-wscite+ACI- available for Windows and e.g. Linux, which can set the 
end-of-lign-sign the way You need it. You should have a look, wether the 
line before the ones You posted here:
+AD4APg- Fatal error: number of coordinate file +ADw-cm5+AF8-b4ion.gro, 28016+AD4- does 
+AD4APg- not
+AD4APg- match tobology +ADw-topol.top, 0 +AD4-
showed some wired spellings, this would then realy point to such a 
simple syntax problem.
Greetings, Marco.

Marco Moeller
Molekulare Biophysik
Universitaet Mainz

----- Original Message ----- 
From: +ACI-Florian Haberl+ACI- +ADw-Florian.Haberl+AEA-chemie.uni-erlangen.de+AD4-
To: +ACI-Vlad Scepanovsky+ACI- +ADw-jaguar1+AEA-ukr.net+AD4AOw- +ACI-Discussion list for GROMACS 
users+ACI- +ADw-gmx-users+AEA-gromacs.org+AD4-
Sent: Wednesday, March 23, 2005 5:35 PM
Subject: Re: +AFs-gmx-users+AF0- Fatal error: number of coordinate file 
+ADw-cm5+AF8-b4ion.gro,28016+AD4- does not match

+AD4- Hi,
+AD4APg- I have some problems with creation of my Drug-Enzyme complex 
+AD4APg- topology
+AD4APg- file. I-AEDANS acted as my Drug.
+AD4APg- The coordinate file of I-AEDANS was created by proDRG server.
+AD4APg- While using the instructions +ACI-Gromacs Tutorial for Drug-Enzyme 
+AD4APg- Complex+ACI-
+AD4APg- written by John E. Kerrigan, Ph.D.
+AD4APg- IST/Academic Computing Services
+AD4APg- RWJMS-University of Medicine and Dentistry of NJ
+AD4APg- 675 Hoes Lane, RM SB11
+AD4APg- Piscataway, NJ 08854
+AD4APg- I've got DRGGMX.ITP and renamed it to iae.itp,
+AD4APg- then I used a program pdb2gmx for conversion of my enzyme cm5.pdb to
+AD4APg- cm5.gro The second step was to open DRGFIN.GRO in a text editor and 
+AD4APg- paste
+AD4APg- all of the lines to CM5.GRO.
+AD4APg- Then:
+AD4APg- editconf -bt octahedron -f cm5.gro -o cm5.gro -c -d 1.0
+AD4APg- genbox -cp cm5.gro -cs spc216.gro -o cm5+AF8-b4ion.gro -p topol.top.
+AD4APg- grompp -f em.mdp -c cm5+AF8-b4ion.gro -p topol.top -o cm5+AF8-b4ion.trp.
+AD4APg- The last command is not proceded,
+AD4APg- exactly
+AD4APg- Fatal error: number of coordinate file +ADw-cm5+AF8-b4ion.gro, 28016+AD4- does 
+AD4APg- not
+AD4APg- match tobology +ADw-topol.top, 0 +AD4-
+AD4APg-  Would you be able to help me with this problem?
+AD4APg- Senserely
+AD4APg- yours Vladimir Schepanovsky.
+AD4- Seems your top file got an error, check it if all itp files got loaded 
+AD4- and if
+AD4- number of water is correct, take a look in the last line in the file 
+AD4- perhaps
+AD4- there+AGA-s a missing newline.
+AD4- Greetings,
+AD4- Florian
+AD4- -- 
+AD4- -------------------------------------------------------------------------------
+AD4- Florian Haberl                            Universitaet Erlangen/
+AD4- Computer-Chemie-Centrum    Nuernberg
+AD4-                                                      Naegelsbachstr. 
+AD4- 25
+AD4-                                                      D-91052 Erlangen
+AD4-  Mailto: florian.haberl AT chemie.uni-erlangen.de
+AD4- -------------------------------------------------------------------------------
+AD4- gmx-users mailing list
+AD4- gmx-users+AEA-gromacs.org
+AD4- http://www.gromacs.org/mailman/listinfo/gmx-users
+AD4- Please don't post (un)subscribe requests to the list. Use the
+AD4- www interface or send it to gmx-users-request+AEA-gromacs.org.

More information about the gromacs.org_gmx-users mailing list