Re: [gmx-users] CCl4 parameters
I'll repeat my earlier question: What actually corresponds to line 25? What would the manual indicate about the contents of such a line? That is for you to tell us, so we don't have to sort through your topology. You have everything intact, including line spacing (which doesn't necessarily translate through email). If you can provide the exact line, what it contains, and which section of the topology of which it is a component (pairs, angles, dihedrals, etc) then maybe someone can provide useful advice. If you want free help, make it easy for us to help you. -Justin Hongyan Xiao wrote: Hi, Justin, This is my CCl4.top file. ; ; File 'ccl4.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 9 08:18:55 2008 ; ; This is your topology file ; "God is a DJ" (Faithless) ; ; Include forcefield parameters #include "ffG53a6.itp" #include "ccl4.itp" ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Pure CL4 [ molecules ] ; Compound#mols CL4169 ~ What does it lose? Please give me further suggestion. Thanks again. H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CCl4 parameters
Hi, Justin, This is my CCl4.top file. ; ; File 'ccl4.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 9 08:18:55 2008 ; ; This is your topology file ; "God is a DJ" (Faithless) ; ; Include forcefield parameters #include "ffG53a6.itp" #include "ccl4.itp" ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Pure CL4 [ molecules ] ; Compound#mols CL4169 ~ What does it lose? Please give me further suggestion. Thanks again. H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CCl4 parameters problem
Hongyan Xiao wrote: Hi, all gmx-users, I obtained the gromos96.1 itp file of CCl_ 4 from the PRODRG program and I modified it to agree with the ffG53a6.itp force field parameters. Please see the following, [ moleculetype ] ; Name nrexcl CL4 3 [ atoms ] ;nr type resnr resid atom cgnr charge mass 1 CLCL4 1 CL4 CL1 1 -0.062 35.4530 2 CCL4 1 CL4 CT 10.248 12.0110 3 CLCL4 1 CL4 CL4 1 -0.062 35.4530 4 CLCL4 1 CL4 CL2 1 -0.062 35.4530 5 CLCL4 1 CL4 CL3 1 -0.062 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.176 810.00.176 810.0 ;CT CL1 2 3 20.176 810.00.176 810.0 ;CT CL4 2 4 20.176 810.00.176 810.0 ;CT CL2 2 5 20.176 810.00.176 810.0 ;CT CL3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2109.5618.0109.5618.0 ; CL1 CT CL4 1 2 4 2109.5618.0109.5618.0 ; CL1 CT CL2 1 2 5 2109.5618.0109.5618.0 ; CL1 CT CL3 3 2 4 2109.5618.0109.5618.0 ; CL4 CT CL2 3 2 5 2109.5618.0109.5618.0 ; CL4 CT CL3 4 2 5 2109.5618.0109.5618.0 ; CL2 CT CL3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 1 3 4 2 35.3 334.835.3 334.8 ; impCT CL1 CL4 CL2 However, when I ran the grompp program, it pointed out the following the warning WARNING 1 [file ccl4.top, line 25]: Too few parameters on line (source file toppush.c, line 1499) I had a check the CCl_4 parameters again and did not find the parameter lost. I want to know why the warning occurs? If you're working with the .top, what you've shown is not complete (at the very least, it is missing a call to #include "ffG53a6.itp." What actually corresponds to line 25? What would the manual indicate about the contents of such a line? -Justin I hope for your help! Thanks! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CCl4 parameters problem
Hi, all gmx-users, I obtained the gromos96.1 itp file of CCl4 from the PRODRG program and I modified it to agree with the ffG53a6.itp force field parameters. Please see the following, [ moleculetype ] ; Name nrexcl CL4 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CLCL4 1 CL4 CL1 1 -0.062 35.4530 2 CCL4 1 CL4 CT 10.248 12.0110 3 CLCL4 1 CL4 CL4 1 -0.062 35.4530 4 CLCL4 1 CL4 CL2 1 -0.062 35.4530 5 CLCL4 1 CL4 CL3 1 -0.062 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.176 810.00.176 810.0 ;CT CL1 2 3 20.176 810.00.176 810.0 ;CT CL4 2 4 20.176 810.00.176 810.0 ;CT CL2 2 5 20.176 810.00.176 810.0 ;CT CL3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2109.5 618.0109.5 618.0 ; CL1 CT CL4 1 2 4 2109.5 618.0109.5 618.0 ; CL1 CT CL2 1 2 5 2109.5 618.0109.5 618.0 ; CL1 CT CL3 3 2 4 2109.5 618.0109.5 618.0 ; CL4 CT CL2 3 2 5 2109.5 618.0109.5 618.0 ; CL4 CT CL3 4 2 5 2109.5 618.0109.5 618.0 ; CL2 CT CL3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 1 3 4 2 35.3 334.8 35.3 334.8 ; impCT CL1 CL4 CL2 However, when I ran the grompp program, it pointed out the following the warning WARNING 1 [file ccl4.top, line 25]: Too few parameters on line (source file toppush.c, line 1499) I had a check the CCl4 parameters again and did not find the parameter lost. I want to know why the warning occurs? I hope for your help! Thanks! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
