Re: [gmx-users] error while running pdb2gmx

2013-11-13 Thread Mark Abraham 
Probably the default behaviour of pdb2gmx for termini is not appropriate
for your input. Use pdb2gmx -ter and choose wisely

Mark
On Nov 13, 2013 12:03 PM, "hasthi"  wrote:

> Hello GROMACS users,
>   I have phosphorylated Serine residue in my
> protein (140 residues) of interest, now when I run pdb2gmx I get this
> following error
>
> Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
> while sorting atoms.
>
> I checked aminoacid.rtp, there is no separate entry for OXT there.When I
> did the simulation for the same protein prior phosphorylation I did not get
> this error. What is the reason for this and how should I rectify this
> error?
>
> Please help me with this regard
>
>
> Regards,
> Hasthi
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Re: [gmx-users] error while running pdb2gmx

2013-11-13 Thread Justin Lemkul 



On 11/13/13 6:02 AM, hasthi wrote:

Hello GROMACS users,
   I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error

Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while sorting atoms.

I checked aminoacid.rtp, there is no separate entry for OXT there.When I
did the simulation for the same protein prior phosphorylation I did not get
this error. What is the reason for this and how should I rectify this error?

Please help me with this regard



Presumably you have modified the force field to include the phosphorylated 
residue, correct?   Have you followed every one of the steps shown at 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue?


If you need further help, we will need more information, which will include (at 
minimum):


1. Snippet of the PDB file containing the problematic residue
2. Your exact pdb2gmx command
3. The screen output of pdb2gmx (all of it, not just the error message)

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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