[gmx-users] pdb2gmx

[Justin A. Lemkul]

leila karami wrote:
> there is 1 fatal error in pdb2gmx command about pdb file containing 2 
> separate pdb file (protein:nmr structure, dna: x-ray structure). error 
> :[There were 38 missing atoms in molecule, if you want to use this 
> incomplete topology anyhow, use the option -missing](all of missing 
> atoms are H atom). what do I do instead of -missing option?
> 

If all of the atoms are H, use -ignh and allow pdb2gmx to build in all those 
that are necessary.

-Justin

> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> 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

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