[gmx-users] C-terminus residue name in Gromos43a1
Francesca Vitalini
francesca.vitalini11 at gmail.com
Thu Feb 27 15:49:06 CET 2014
I am using Gromacs 4.5.5. In my residuetypes.dat ACE is correctly listed as
protein residue and pdb2gmx doesn't give any error about protein type.
For clarity I copy here my pdb, the interesting parts of the aminoacids.rtp
file and the pdb2gmx command.
Thank you very much for any help you can give.
#####################################
FROM aminoacids.rtp
#####################################
[ ACE ]
[ atoms ]
CA CH3 0.000 0
C C 0.380 1
O O -0.380 1
[ bonds ]
C CA gb_26
C O gb_4
C +N gb_9
[ angles ]
CA C O ga_30
CA C +N ga_18
O C +N ga_32
[ impropers ]
C CA +N O gi_1
[ ALA ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH3 0.00000 1
C C 0.380 2
O O -0.380 2
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
[ 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
-C N gb_9
[ 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
#####################################
pdb file
#####################################
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
TER
#####################################
pdb2gmx
#####################################
pdb2gmx -f Ac_A_NHMe/Ac_A_NHMe_gromos.pdb -o Ac_A_NHMe/Ac_A_NHMe.gro -p
Ac_A_NHMe/Ac_A_NHMe.top -i Ac_A_NHMe/Ac_A_NHMe.itp -n
Ac_A_NHMe/Ac_A_NHMe.ndx -q Ac_A_NHMe/Ac_A_NHMe.pdb -ignh -ter
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) pdb2gmx (-:
Option Filename Type Description
------------------------------------------------------------
-f Ac_A_NHMe/Ac_A_NHMe_gromos.pdb Input Structure file: gro g96
pdb
tpr etc.
-o Ac_A_NHMe/Ac_A_NHMe.gro Output Structure file: gro g96 pdb etc.
-p Ac_A_NHMe/Ac_A_NHMe.top Output Topology file
-i Ac_A_NHMe/Ac_A_NHMe.itp Output Include file for topology
-n Ac_A_NHMe/Ac_A_NHMe.ndx Output, Opt! Index file
-q Ac_A_NHMe/Ac_A_NHMe.pdb Output, Opt! Structure file: gro g96 pdb etc.
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-chainsep enum id_or_ter Condition in PDB files when a new chain
should
be started (adding termini): id_or_ter,
id_and_ter, ter, id or interactive
-merge enum no Merge multiple chains into a single
[moleculetype]: no, all or interactive
-ff string select Force field, interactive by default. Use -h for
information.
-water enum select Water model to use: select, none, spc, spce,
tip3p, tip4p or tip5p
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool yes Interactive termini selection, instead of
charged
(default)
-[no]lys bool no Interactive lysine selection, instead of charged
-[no]arg bool no Interactive arginine selection, instead of
charged
-[no]asp bool no Interactive aspartic acid selection, instead of
charged
-[no]glu bool no Interactive glutamic acid selection, instead of
charged
-[no]gln bool no Interactive glutamine selection, instead of
neutral
-[no]his bool no Interactive histidine selection, instead of
checking H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond
(nm)
-[no]una bool no Select aromatic rings with united CH atoms on
phenylalanine, tryptophane and tyrosine
-[no]ignh bool yes Ignore hydrogen atoms that are in the coordinate
file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes Use charge groups in the .rtp file
-[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file)
-[no]renum bool no Renumber the residues consecutively in the
output
-[no]rtpres bool no Use .rtp entry names as residue names
Select the Force Field:
>From current directory:
1: GROMOS96 43a1 force field
>From '/usr/share/gromacs/top':
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (with CMAP) - version 2.0
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
16: [DEPRECATED] Encad all-atom force field, using full solvent charges
17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum
charges
18: [DEPRECATED] Gromacs force field (see manual)
19: [DEPRECATED] Gromacs force field with hydrogens for NMR
1
Using the Gromos43a1_modifiedwithNAC force field in directory
./gromos43a1_modifiedwithNAC.ff
Opening force field file ./gromos43a1_modifiedwithNAC.ff/watermodels.dat
Select the Water Model:
1: SPC simple point charge, recommended
2: SPC/E extended simple point charge
3: None
1
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.r2b
Reading Ac_A_NHMe/Ac_A_NHMe_gromos.pdb...
Read 'ACETYL-ALANINE-METHYLAMIDE', 10 atoms
Back Off! I just backed up Ac_A_NHMe/Ac_A_NHMe.pdb to
Ac_A_NHMe/#Ac_A_NHMe.pdb.5#
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 0 residues with 10 atoms
chain #res #atoms
1 'A' 1 1
2 ' ' 3 9
All occupancies are one
Opening force field file ./gromos43a1_modifiedwithNAC.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos43a1_modifiedwithNAC)
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.rtp
Residue 97
Sorting it all out...
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.hdb
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.n.tdb
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.c.tdb
Back Off! I just backed up Ac_A_NHMe/Ac_A_NHMe.top to
Ac_A_NHMe/#Ac_A_NHMe.top.5#
Processing chain 1 'A' (1 atoms, 1 residues)
Identified residue ACE1 as a starting terminus.
Identified residue ACE1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
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
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1034
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
-------------------------------------------------------
Francesca
2014-02-27 11:59 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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" <jalemkul at 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 <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.
>>>>
>>>>
>>>> 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
>>>
>>> jalemkul at 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-request at 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
>
> jalemkul at 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
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>
--
Francesca Vitalini
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