[gmx-users] introducing "HISE" to gromos43a1

[Justin Lemkul]

On 1/25/14, 3:11 PM, Sajad Ahrari wrote:
> in fact Tyr363 is the C-terminus and the command is;
> pdb2gmx -f  MARKII.pdb  -o  MARKII.gro  -p  MARKII.top
> I have TPO (phospho-threonie 208) as the non-standards amino-acid. so i used
> your introduced "gromos43a1p.ff" for pdb2gmx command.
>

pdb2gmx should replace the OXT it finds with O2, per the *.c.tdb file.  What 
happens if you rename OXT to O2 or remove it altogether?

-Justin

>
> On Saturday, January 25, 2014 11:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/25/14, 11:04 AM, Saman Shahriyari wrote:
>  > dear Justin
>  > thank you for answering. your instruction with "aminoacids.r2b file", helped.
>  > this time i am having the following problem;
>  > Program pdb2gmx, VERSION 4.6.3
>  > Source code file: /usr/local/Software/gromacs-4.6.3/src/kernel/pdb2gmx.c,
> line: 727
>  > Fatal error:
>  > Atom OXT in residue TYR 363 was not found in rtp entry TYR with 18 atoms
>  > while sorting atoms.
>  >
>  > any suggestion on dealing with OXT?
>
> pdb2gmx thinks Tyr363 is the C-terminus.  Is that correct?  What is your exact
> command line?  Do you have any nonstandard residues?
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> <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
> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>or send a
> mail to gmx-users-request at gromacs.org. <mailto:gmx-users-request at gromacs.org.>
>
>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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