[gmx-users] pull.ppa doesn't work

[Justin A. Lemkul]

accomp lin wrote:
> <http://www.mdbbs.org/tag-pull.html>
> hi everyone,
> 
> I;m using umbrella sampling to calculate PMF
> 
> My system is DPPC + water + protein
> In pull.ppa, I set runtype = umbrella ，reftype = com_t0，
> K1   = 5000  ，Pos1  = 0.0 0.0 6.0
> 
> However this came out when I finally type mdrun :
>  
> 
> Reading parameter file pull.ppa
> ' for variable verbose, using 'no'
> Next time use one of : 'no' 'yes'
> ' for variable runtype, using 'afm'
> Next time use one of : 'afm' 'constraint' 'umbrella'
> ' for variable reftype, using 'com'
> Next time use one of ; 'com' 'com_t0' 'dynamic' 'dynamic_t0'
> .....................
> .....................
> .....................
>  

Then something is badly formatted in the file.  Perhaps it was edited on a 
Windows machine and has hidden formatting characters?

> ——————————————————————————————
> program mdrun, VERSION 3.3.3
> source code file: pullinit.c, line: 215
> 
> Fatal error:
> in the index fileGN
> ——————————————————————————————
> 
> It seems that mdrun doesn't recognize what I set in pull.ppa
> And I don't know what's wrong with my index file, it looks all right to me.
> So, can any body tell me what is going on?

Could also be related to the same formatting issues you're seeing with your .ppa 
file.

-Justin

>  
> Thanks!
> 
> 
> ------------------------------------------------------------------------
> 好玩贺卡等你发，邮箱贺卡全新上线！ 
> <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================