[gmx-users] question
Justin Lemkul
jalemkul at vt.edu
Tue May 19 17:29:16 CEST 2015
On 5/19/15 11:19 AM, Andrew Bostick wrote:
> Dear Tsjerk, Justin and Mark
>
> Very thanks for your answers and guidance.
>
> I installed gromacs 5.0.5. I used gmx pdb2gmx -f be_near.pdb -ignh -merge
> all.
>
> I want to have a link between two chains (CD atom of GLU residue from
> chaim B and NZ atom of LYS residue from chain E) to get isopeptide bond
> between these two atoms. I used the all for -merge option. Is this true?
> After gmx pdb2gmx, I encountered with:
>
> Linking CYS-252 SG-248 and CYS-312 SG-743...
> Linking CYS-358 SG-1094 and CYS-416 SG-1565...
> Linking GLU-380 CD-1269 and LYS-540 NZ-2499...
> Start terminus PRO-220: PRO-NH2+
> End terminus HIS-434: COO-
> Start terminus GLY-435: GLY-NH3+
> End terminus LYS-551: COO-
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 332 residues with 3314 atoms
> Making bonds...
>
> WARNING: atom H is missing in residue GLU 380 in the pdb file
> You might need to add atom H to the hydrogen database of building
> block GLU2
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom H is missing in residue LYS 540 in the pdb file
> You might need to add atom H to the hydrogen database of building
> block LYS2
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file
> You might need to add atom HZ1 to the hydrogen database of
> building block LYS2
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file
> You might need to add atom HZ2 to the hydrogen database of
> building block LYS2
> in the file aminoacids.hdb (see the manual)
> ------------------------------------------------------
> Program gmx, VERSION 5.0.5
> Source code file:
> /export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp,
> line: 1587
>
> Fatal error:
> There were 4 missing atoms in molecule Protein_chain_B, if you want to use
> this incomplete topology anyhow, use the option -missing
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ------------------------------------------------------
>
> I added following lines to aminoacids.hdb file of gromose43a1 force field.
>
> LYS2 2
> 1 1 H N -C CA
> 2 4 HZ NZ CE CD
>
You don't want to be adding 2 HZ here, just one since it is a peptide bond.
> GLU2 1
> 1 1 H N -C CA
>
> Then, this error was solved. Is my manner true?
>
> Then, I checked topology file:
>
> ; residue 380 GLU rtp GLU2 q 0.0
> 1595 N 380 GLU N 705 -0.28 14.0067 ;
> qtot -2.28
> 1596 H 380 GLU H 705 0.28 1.008 ;
> qtot -2
> 1597 CH1 380 GLU CA 706 0 13.019 ;
> qtot -2
> 1598 CH2 380 GLU CB 706 0 14.027 ;
> qtot -2
> 1599 CH2 380 GLU CG 706 0 14.027 ;
> qtot -2
> 1600 C 380 GLU CD 707 0.38 12.011 ;
> qtot -1.62
> 1601 OM 380 GLU OE1 707 -0.38 15.9994 ;
> qtot -2
> 1602 OM 380 GLU OE2 707 0 15.9994 ;
> qtot -2
> 1603 C 380 GLU C 708 0.38 12.011 ;
> qtot -1.62
> 1604 O 380 GLU O 708 -0.38 15.9994 ;
> qtot -2
>
> and
>
> ; residue 540 LYS rtp LYS2 q 0.0
> 3198 N 540 LYS N 1422 -0.28 14.0067 ;
> qtot -5.28
> 3199 H 540 LYS H 1422 0.28 1.008 ;
> qtot -5
> 3200 CH1 540 LYS CA 1423 0 13.019 ;
> qtot -5
> 3201 CH2 540 LYS CB 1423 0 14.027 ;
> qtot -5
> 3202 CH2 540 LYS CG 1424 0 14.027 ;
> qtot -5
> 3203 CH2 540 LYS CD 1424 0 14.027 ;
> qtot -5
> 3204 CH2 540 LYS CE 1424 0 14.027 ;
> qtot -5
> 3205 NT 540 LYS NZ 1425 -0.28 14.0067 ;
> qtot -5.28
> 3206 H 540 LYS HZ1 1425 0.28 1.008 ;
> qtot -5
> 3207 H 540 LYS HZ2 1425 0 1.008 ;
> qtot -5
> 3208 C 540 LYS C 1426 0.38 12.011 ;
> qtot -4.62
> 3209 O 540 LYS O 1426 -0.38 15.9994 ;
> qtot -5
>
> Then, I did following steps:
>
> gmx editconf -f conf.gro -o box.gro -d 0.8 -bt cubic -c
> gmx solvate -cp box.gro -cs spc216.gro -p topol.top -o sol.gro
> gmx grompp -f ions.mdp -c sol.gro -p topol.top -o ions.tpr
>
> After using last command, I encountered with:
>
> NOTE 1 [file ions.mdp]:
> With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> that with the Verlet scheme, nstlist has no effect on the accuracy of
> your simulation.
>
> Setting the LD random seed to 1332188956
> Generated 279 of the 1225 non-bonded parameter combinations
>
> ERROR 1 [file topol.top, line 5321]:
> No default G96Bond types
>
>
> ERROR 2 [file topol.top, line 14911]:
> No default G96Angle types
>
>
> ERROR 3 [file topol.top, line 14913]:
> No default G96Angle types
>
>
> ERROR 4 [file topol.top, line 14914]:
> No default G96Angle types
>
>
> ERROR 5 [file topol.top, line 17318]:
> No default G96Angle types
>
>
> ERROR 6 [file topol.top, line 17319]:
> No default G96Angle types
>
>
> ERROR 7 [file topol.top, line 17320]:
> No default G96Angle types
>
>
> ERROR 8 [file topol.top, line 18389]:
> No default Proper Dih. types
>
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 2 [file topol.top, line 21025]:
> System has non-zero total charge: -5.999997
> Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
> Removing all charge groups because cutoff-scheme=Verlet
>
> There were 2 notes
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.5
> Source code file:
> /export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxpreprocess/grompp.c,
> line: 1724
>
> Fatal error:
> There were 8 errors in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Please see the fig_1.png in following link:
>
> https://www.dropbox.com/s/y22obrx3wjg8en9/fig_1.png?dl=0
>
> Before, I had a qestion in
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097387.html
> .
>
> "hould I need to change force field parameters?"
>
> Justin answered me:
>
> "This is just a peptide bond; all force fields will have the needed
> parameters."
>
> What is the reason of above error (Bond, Angle and Proper Dih. types)?
>
You have NT as the Lys NZ atom type rather than N, which is the correct type for
a peptide bond (just like the backbone).
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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