Re: [gmx-users] grompp errors..

2012-09-29 Thread Justin Lemkul
On 9/29/12 12:55 PM, Ali Alizadeh wrote: Dear All users I have a system with 3 layers, when i run grompp program, encounter with this error. First and 3th layer is the same, and middle layer is water. what's this error about? grompp is looking for some group called "1" (the number one) but i

Re: [gmx-users] grompp errors

2011-09-20 Thread Justin A. Lemkul
Please use an informative subject. ITHAYARAJA wrote: Dear Sir, when i am doing energy minimization (grompp), i found following error CMD : grompp -f em.mdp -c proteinGR_b4ion.gro -p proteinGR.top -o proteinGR_b4ion.tpr WARNING 1 [file em.mdp, line unknown]: Unknown or double left-hand 'c

Re: [gmx-users] grompp errors

2010-07-13 Thread David van der Spoel
On 7/13/10 6:11 PM, Amanda Watkins wrote: Tue, July 13, 2010 11:46:58 AM grompp errors ... From: Amanda Watkins [Chat now] ... View Contact To: gmx-users@gromacs.org Dear GROMACS users, I am trying to simulate a

Re: [gmx-users] grompp errors

2010-07-13 Thread Justin A. Lemkul
Amanda Watkins wrote: Tue, July 13, 2010 11:46:58 AM grompp errors ... From: Amanda Watkins [Chat now] ... View Contact To: gmx-users@gromacs.org Dear GROMACS users, I am trying to simulate a protein (OmpA) a

[gmx-users] grompp errors

2010-07-13 Thread Amanda Watkins
Tue, July 13, 2010 11:46:58 AM grompp errors... From: Amanda Watkins ...View Contact To: gmx-users@gromacs.org Dear GROMACS users, I am trying to simulate a protein (OmpA) and a detergent (DPC) together in GROMACS. I have successfully generate and minimized

Re: [gmx-users] grompp errors

2009-03-30 Thread Tsjerk Wassenaar
No. Even though you give the grompp output, you haven't told what you tried to do, which force field you're using and what you did to come to this stage. We can't guess what's in you're topology file. You also clearly haven't searched the archive for posts on "No default ... types", and thus give

[gmx-users] grompp errors

2009-03-30 Thread andrea . borgogno
i have a problem with gromp someone can elp me? thanks.. error_grompp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

[gmx-users] Grompp errors?

2006-06-26 Thread Jones de Andrade
Hi all!. I was trying to simulate a complex cation in MeCN solution and I got 2 strange warnings to me: processing topology... WARNING 1 [file "ff_emi.itp", line 7]: Overriding atomtype CT WARNING 2 [file "ff_emi.itp", line 11]: Overriding atomtype H1 But I did found that strange because, as