On 2/27/14, 2:03 AM, Francesca Vitalini wrote:
Residue 2 is just alanine,the most standard amino acid ever.
What Gromacs version is this? Is ACE correctly listed in residuetypes.dat as a
protein residue? pdb2gmx will also tell you this if it warns that residue 1 and
2 are not of the same type.
-Justin
Any help?
Francesca.
Il 26/feb/2014 11:58 "Justin Lemkul" <jalem...@vt.edu> ha scritto:
On 2/26/14, 4:08 AM, Francesca Vitalini wrote:
Dear Justin
2014-02-25 19:07 GMT+01:00 Justin Lemkul <jalem...@vt.edu>:
On 2/25/14, 12:56 PM, Francesca Vitalini wrote:
Dear Justin,
Thanks for your answer.
However I noticed that I had made a mistake and there is no definition
of
NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at.
So defining a new residue-type in the rtp file is not as trivial as I
had
hoped.
I followed the instructions given on the GROMACS wab page
http://www.gromacs.org/Documentation/How-tos/Adding_
a_Residue_to_a_Force_Field
and copied the gromos43a1.ff folder and the residuetypes.dat file in my
local directory.
I have added the following definition of NAC to the
gromos43a1.ff/aminoacids.rtp file
[ NAC ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH3 0.00000 0
[ bonds ]
N CA gb_20
N H gb_2
You're missing a bond here, from N to -C.
I hadn't add that as all the other residue types also don't have it
defined. It seems to me that the bond is defined as C to N+ not the other
way round. In this case however I have no N+ and the hydrogens are not
defined, so how can I properly define that bond?
I also tried to define the bond N to -C as gb_9 (ie the bond type of C to
N+) but it leads to the exact same error message.
Ah, true, this isn't necessary.
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
and then tried again the pdb2gmx command as following and obtained this
error
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
Evidently I have not defined correctly my NAC residue. However, I am not
sure of how to correctly define the bonds in this specific case. Could
you
possibly identify the error and/or point me where to find detailed
information? I have already looked at the manual but haven't been able
to
come up with successful definition.
You need to use pdb2gmx -ter and select "None" for the C-terminus,
otherwise pdb2gmx tries to build a carboxylate. When it can't find the
atoms it needs to do this, it fails.
I do use the -ter "None" option for both termini and the error is still
present. What I find interesting is this part of the pdb2gmx output
Select start terminus type for ACE-1
0: NH3+
1: NH2
2: None
2
Start terminus ACE-1: None
Select end terminus type for ACE-1
0: COO-
1: COOH
2: None
2
End terminus ACE-1: None
where it looks like that ACE is the end terminus, not NAC, despite my pdb
looks like the following. Any suggestions?
What is residue 2? Is it anything non-standard?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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-requ...@gromacs.org.
