[gmx-users] KALP-15 in DPPC tutorial

[RINU KHATTRI]

check your popc128.top
or topol.top file
 ; Include POPC chain topology
#include "popc.itp"

and
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
and always update the no of atoms in you .gro file

On Mon, Mar 16, 2015 at 10:31 AM, RINU KHATTRI <nickname.mittu at gmail.com> wrote:
> firstly go back to check your system.gro file which you made bu cat
> DPPC.gro new_box.gro >system.gro
> remove some line between the merging of two file update the no of atoms
> then do your next step
>
>
> On Mon, Mar 16, 2015 at 9:38 AM, BAOLIN HUANG <baolin.huang at qut.edu.au> wrote:
>> Hi All,
>> I am doing the GROMACS Tutorial of KALP-15 in DPPC.
>> Now, I get stuck at "Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat"
>>
>> The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I got Fatal error: No such moleculetype DPPC.
>>
>> How to update the [molecules] in topol.top? And how do I know the number of molecules?
>>
>>
>>
>> Kind regards,
>>
>> Alex Huang
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.