[gmx-users] C-terminus residue name in Gromos43a1
Francesca Vitalini
francesca.vitalini11 at gmail.com
Tue Feb 25 18:56:17 CET 2014
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
[ 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.
Thank you very much.
Best,
Francesca
pdb2gmx -f Ac_A_NHMe/Ac_A_NHMe.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 (-:
GROningen MAchine for Chemical Simulation
:-) 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.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.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.7#
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.7#
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
-------------------------------------------------------
"I'm Looking for a New Simulation" (Stone Temple Pilots)
2014-02-24 19:11 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 2/24/14, 5:35 AM, Francesca Vitalini wrote:
>
>> Dear Gromacs Users,
>>
>> does anybody know the residue name for the c-terminus NHMe in Gromos43a1.
>> I
>> tried NAC that works for GROMOS53 but it doesn't exist in the
>> /gromos43a1.ff/aminoacids.rtp and there I couldn't find the correct name.
>> However, it seems improbable that such a standard thing is not implemented
>> by default.
>>
>
> It's not improbable at all; the force fields are updated individually, so
> changes in one may not be reflected in the others.
>
>
> If anyone has previously used it, could you please let me know how to
>> introduce it correctly in my pdb structure so that it is recognized by
>> pdb2gmx?
>>
>>
> It's fairly straightforward to use the 53A6 .rtp entry as a basis for
> 43A1. The only difference will be the charges on N and H that need to be
> changed to agree with 43A1 backbone charges.
>
> -Justin
>
>
> So far I get this error message
>>
>> Program pdb2gmx, VERSION 4.5.5
>> Source code file: /tmp/build/gromacs-4.5.5/src/kernel/resall.c, line: 581
>>
>> Fatal error:
>> Residue 'NAC' not found in residue topology database
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> Thank you very much,
>>
>> Francesca
>>
>>
> --
> ==================================================
>
> 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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--
Francesca Vitalini
Freie Universität Berlin
Institute for Chemistry and Biochemistry
Physical & Theoretical Chemistry
35.20
Takustraße 3
14195 Berlin
Germany
vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de
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