[gmx-users] C-terminus residue name in Gromos43a1
Francesca Vitalini
francesca.vitalini11 at gmail.com
Wed Feb 26 10:08:25 CET 2014
Dear Justin
2014-02-25 19:07 GMT+01:00 Justin Lemkul <jalemkul at 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.
>
> [ 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?
Thanks
Francesca
TITLE ACETYL-ALANINE-METHYLAMIDE
REMARK GENERATED BY CUTTING OUT RESIDUE 14 TO 16 FROM FROM 2KSZ.PDB SEQ 1
MODEL 1
ATOM 1 1HH3 ACE A 1 9.955 -1.448 -7.763 1.00
0.00 H
ATOM 2 CA ACE A 1 10.830 -2.612 -7.822 1.00 0.00
C
ATOM 3 C ACE A 1 10.355 -3.683 -6.846 1.00
0.00 C
ATOM 4 O ACE A 1 10.264 -4.861 -7.196 1.00
0.00 O
ATOM 5 2HH3 ACE A 1 12.264 -2.204 -7.476 1.00
0.00 H
ATOM 6 3HH3 ACE A 1 10.814 -3.010 -8.826 1.00
0.00 H
ATOM 7 N ALA A 2 10.042 -3.264 -5.625 1.00
0.00 N
ATOM 8 CA ALA A 2 9.563 -4.193 -4.609 1.00
0.00 C
ATOM 9 C ALA A 2 8.170 -4.706 -4.969 1.00
0.00 C
ATOM 10 O ALA A 2 7.806 -5.832 -4.630 1.00
0.00 O
ATOM 11 CB ALA A 2 9.507 -3.492 -3.251 1.00
0.00 C
ATOM 12 H ALA A 2 10.127 -2.310 -5.408 1.00
0.00 H
ATOM 13 HA ALA A 2 10.248 -5.025 -4.538 1.00
0.00 H
ATOM 14 HB1 ALA A 2 9.115 -4.175 -2.509 1.00
0.00 H
ATOM 15 HB2 ALA A 2 8.867 -2.625 -3.317 1.00
0.00 H
ATOM 16 HB3 ALA A 2 10.502 -3.185 -2.963 1.00
0.00 H
ATOM 17 N NAC A 3 7.398 -3.868 -5.656 1.00
0.00 N
ATOM 18 CA NAC A 3 6.046 -4.242 -6.057 1.00
0.00 C
ATOM 19 1HH3 NAC A 3 6.078 -5.329 -7.127 1.00
0.00 H
ATOM 20 2HH3 NAC A 3 5.308 -3.015 -6.599 1.00
0.00 H
ATOM 21 H NAC A 3 7.743 -2.984 -5.899 1.00
0.00 H
ATOM 22 3HH3 NAC A 3 5.512 -4.613 -5.197 1.00
0.00 H
~
~
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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