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<DIV><FONT face=Tahoma>No. I only changed 3 lines in ffgmxnb.itp. But there are
hundreds of lines of error informaion like this:</FONT></DIV>
<DIV><FONT face=Tahoma>ERROR 77 [file ffgmxnb.itp, line 144]:<BR> Trying
to add LJ (SR) while the default nonbond type is Buck.ham (SR)</FONT></DIV>
<DIV> </DIV><FONT face=Tahoma>
<DIV><BR>ERROR 78 [file ffgmxnb.itp, line 145]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV> </DIV>
<DIV><BR>ERROR 79 [file ffgmxnb.itp, line 146]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV> </DIV>
<DIV><BR>ERROR 80 [file ffgmxnb.itp, line 147]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV> </DIV>
<DIV><BR>ERROR 81 [file ffgmxnb.itp, line 148]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV> </DIV>
<DIV><BR>ERROR 82 [file ffgmxnb.itp, line 149]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV> </DIV>
<DIV><BR>ERROR 83 [file ffgmxnb.itp, line 150]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV> </DIV>
<DIV><BR>ERROR 84 [file ffgmxnb.itp, line 151]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV> </DIV>
<DIV><BR>ERROR 85 [file ffgmxnb.itp, line 152]:<BR> Trying to add LJ (SR)
while the default nonbond type is Buck.ham (SR)</DIV>
<DIV></FONT> </DIV>
<BLOCKQUOTE
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="FONT: 10pt arial; BACKGROUND: #e4e4e4; font-color: black"><B>From:</B>
<A title=gmx3@hotmail.com href="mailto:gmx3@hotmail.com">Berk Hess</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Sunday, February 22, 2009 3:03
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> RE: [gmx-users] combination
rules -- the part aboutthecombinationrules</DIV>
<DIV><BR></DIV>Hi,<BR><BR>Is line 68 one of the lines you have added, or
another one?<BR><BR>Berk<BR><BR>> From: <A
href="mailto:shuangxingdai@gmail.com">shuangxingdai@gmail.com</A><BR>> To:
<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>>
Subject: Re: [gmx-users] combination rules -- the part aboutthe
combinationrules<BR>> Date: Sun, 22 Feb 2009 14:55:21 -0700<BR>>
<BR>> Thank you. I have referred to the manual and changed these parts as
the <BR>> manual told me:<BR>> in ffgmx.itp:<BR>> [ defaults
]<BR>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<BR>> 2 1 no 1.0
1.0<BR>> <BR>> in ffgmxnb.itp:<BR>> [ nonbond_params ]<BR>> ; i j
func a b c6<BR>> O O 2 92137.86 45.62876437 3090<BR>> ZN O 2 51108.27
27.92516056 0<BR>> ZN ZN 2 0 0.1 0<BR>> But there is no change in the
generated .top file.<BR>> When I use grompp, the errors are :<BR>> ERROR
1 [file ffgmxnb.itp, line 68]:<BR>> Trying to add LJ (SR) while the default
nonbond type is Buck.ham (SR)<BR>> Maybe somewhere else need to be changed.
Anyone knows why and how?<BR>> Thank you in advance.<BR>> <BR>> -----
Original Message ----- <BR>> From: "Mark Abraham"
<Mark.Abraham@anu.edu.au><BR>> To: "Discussion list for GROMACS
users" <gmx-users@gromacs.org><BR>> Sent: Friday, February 20, 2009
6:02 PM<BR>> Subject: Re: [gmx-users] combination rules -- the part
aboutthe <BR>> combinationrules<BR>> <BR>> <BR>> > Shuangxing
Dai wrote:<BR>> >> Thanks for your answer. I changed the non-bond
parameters in ffgmxnb.itp. <BR>> >> like<BR>> >> ; i j func
a b c6<BR>> >> Zn O 2 ... ..... .... But error occured..<BR>>
>><BR>> >> ERROR 1 [file ffgmxnb.itp, line 270]:<BR>>
>><BR>> >> Trying to add Buck.ham (SR) while the default
nonbond type is LJ (SR)<BR>> >><BR>> >> ERROR 2 [file
ffgmxnb.itp, line 271]:<BR>> >><BR>> >> Trying to add
Buck.ham (SR) while the default nonbond type is LJ (SR)<BR>>
>><BR>> >> ERROR 3 [file ffgmxnb.itp, line 272]:<BR>>
>><BR>> >> Trying to add Buck.ham (SR) while the default
nonbond type is LJ (SR)<BR>> >><BR>> >> I think I have
indicated that the function type is 2 (means Buckingham). <BR>> >>
Anything else need to do with this ?<BR>> ><BR>> > ... specify
that the default nonbonded type is not LJ? Have a look in <BR>> >
Chapter 5 of the manual.<BR>> ><BR>> >> Also, I want to fix
some atoms in the boundary and specify displacement <BR>> >> to some
atoms, anayone knows how to do this?<BR>> ><BR>> > You can freeze
groups of atoms, or use position restraints, or pull groups <BR>> > of
atoms, but you should look first in the manual for the information that
<BR>> > is there.<BR>> ><BR>> > Mark<BR>> >
_______________________________________________<BR>> > gmx-users mailing
list gmx-users@gromacs.org<BR>> >
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