[gmx-users] problem with ffamber94bon.itp
adriana at ms.fci.unibo.it
Fri Apr 28 17:41:06 CEST 2006
Hi all and thanks to Tom and Erick for your reply.
I tried this option:
and there are no more warning,
on the contrary I have not clear that in the file ffambernb.itp the charge
are 0.00 and also the mass, that I manually wrote, I mean:
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
amber94_1 BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00
amber94_2 C 0.00000 0.0000 A 3.39967e-01 3.59824e-01
amber94_3 CA 0.00000 0.0000 A 3.39967e-01 3.59824e-01
and I manually wrote only the masses, not the charges,
Anyone knows if this could generate problems with MD?
thanks in advance,
> Hi Tom,
> I'm not sure if it works, but if you are using gcc you could try
> setting this in your mdp file:
> cpp = "cpp -traditional-cpp"
> Or, -no-traditional-cpp - I never remember which flag is which...
> On Apr 28, 2006, at 3:53 PM, Tomas Kubar wrote:
> > hi
> > the file ffamber94bon.itp defines the parameters as macros. some of
> > the macro names contain an asterisk character (*), e.g.
> > #define proper_X_CT_N*_X 0.00000 0.00000 0.00000
> > 0.00000 0.00000 0.00000
> > this makes the preprocessor issue a warning (no whitespace after
> > macro name) because a macro name is not allowed to contain this
> > character. it looks like this might lead to wrong macro expansion
> > in case this dihedral is contained in the molecule's topology.
> > right now, I don't have an idea how to fix this...
> > tom
> > Adriana Pietropaolo wrote:
> >> Dear gmx users,
> >> I have some problems to use amber force field.
> >> When I try to use grompp with a topology created with ffamber* (I
> >> download each files from the gromacs home page) there are these
> >> errors:
> >> missing terminating ' character
> >> ffamber94bon.itp:384:116: missing terminating ' character
> >> ffamber94bon.itp:385:116: missing terminating ' character
> >> ffamber94bon.itp:391:116: missing terminating ' character
> >> ffamber94bon.itp:423:23: warning: ISO C requires whitespace after
> >> the macro nameffamber94bon.itp:425:23: warning: ISO C requires
> >> whitespace after the macro nameffamber94bon.itp:426:23: warning:
> >> ISO C requires whitespace after the macro nameffamber94bon.itp:
> >> 429:22: warning: ISO C requires whitespace after the macro
> >> nameffamber94bon.itp:438:20: warning: ISO C requires whitespace
> >> after the macro namecpp exit code: 256
> >> I found in the web some similar posts but I did not find any reply.
> >> Would you suggest me some advice?
> >> Thank you for your kind attention,
> >> cheers,
> >> Adriana
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
More information about the gromacs.org_gmx-users