[gmx-users] Gromax don't recognize -ignh command

[Justin Lemkul]

On 12/29/19 2:54 PM, Mark Abraham wrote:
> Hi,
>
> I expect that's a hydrogen in an NH3+ group being added as a terminus to
> your protein.  You might want to tell pdb2gmx to stop trying to help with
> the termini, with -ter or -noter.

HA3 isn't a terminal proton in the CHARMM force field so I doubt that's 
it. The full screen output from pdb2gmx would be informative here.

-Justin

> Mark
>
> On Sun, 29 Dec 2019 at 13:02, ali khamoushi <khamuoshia at gmail.com> wrote:
>
>> Hello everyone
>> I have PDB file which have directly downloaded from RCSB.org
>> but when I want to do the procedure of simulation, I get this error:
>> Fatal error:
>> Atom HA3 in residue GLY 1 was not found in rtp entry GLY with 9 atoms
>> while sorting atoms.
>>
>> I have searched and find that the solution is to run the -ignh command. but
>> gromacs does'nt recognize it.
>> my code for first step is:
>> ‫‪gmx‬‬ ‫‪pdb2gmx‬‬ ‫‪-f‬‬ ‫‪protein-nolig.pdb‬‬ ‫‪-water‬‬ ‫‪tip3p‬‬
>> ‫‪-ignh‬‬ ‫‪-o‬‬ ‫‪conf.gro‬‬
>> or this:
>>
>> gmx pdb2gmx -f protein.pdb -o protein.gro‬‬ -water tip3p -ignh
>>
>> but neither is working.
>> my forcefield is charmm36 and changing the forcefield didn't help.
>> --
>> 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.

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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