[gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic
Elisa Pieri
elisa.pieri at univ-amu.fr
Thu Oct 26 13:06:05 CEST 2017
Thank you very much for the answers! We made the modifications you
suggested and now the error changed.
Now we have this problem: we have an ALA residue, linked to a LYS. The LYS
is linked to a retinal moiety; for this, we created a "new" residue called
"RET" which includes LYS+retinal. But now, Gromacs is seeing the ALA as a
terminal residue and is adding an oxygen, witouh making the the link
between ALA and RET. I suppose we have to add some parameters, but we
couldn't really figure out which ones. Could you help us?
Elisa
On Thu, Oct 26, 2017 at 12:01 PM, Piggot T. <T.Piggot at soton.ac.uk> wrote:
> In the line you have added into the ffnonbonded.itp it looks like the
> numbers for the LJ parameters have a comma rather than a point. So
> 2,47135e-01 rather than 2.47135e-01. I imagine this is causing the too few
> parameters on line warning
>
> Cheers
>
> Tom
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Elisa
> Pieri [elisa.pieri at univ-amu.fr]
> Sent: 26 October 2017 10:53
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic
>
> Hello again,
>
> we are trying to add Amber lipids to the Amber94 force field (actually, it
> is a version where a few years ago we added a ligand). We used pdb2gmx as
> "pdb2gmx -f file.pdb" and we successfully created a conf.gro and topol.top
> file (and posre.itp and top.itp per lipid molecule). Then, when we tried to
> used grompp as "grompp -f file.mdp -p topol.top -c conf.gro -o conf.tpr",
> we got many warnings of the type
>
> This is an example of the warnings:
> WARNING 15 [file ffnonbonded.itp, line 78]: Too few parameters on line
> (source file /home/people/Downloads/gromacs-5.1.4/src/gromacs/
> gmxpreprocess/toppush.c,
> line 338)
>
> And a fatal error:
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
> line: 742
> Fatal error: Unknown bond_atomtype hE
>
> I'm showing you what additions we made (in particular, for hE).
> We added the new atomtypes (20) in the atomtypes.atp file in the form:
> hE 1.00800 ; lipid H bonded to aliphatic carbon with 1
> electron withdrawing group
>
> Then we added the parameters in the ffbonded.itp file; example of
> stretching, bendind and torsions for hE:
>
> cA hE 1 0.10930 281081.1 ; lipid
>
> cA cA hE 1 110.070 387.940
> cB cA hE 1 110.460 393.547
> hE cA hE 1 109.550 327.858
> hE cA nN 1 109.500 416.559
> hE cA oH 1 109.880 426.517
> hE cA oS 1 108.820 425.429
> hE cA oT 1 109.500 418.400
>
> cA cA cA hE 9 0.0 0.65103 3
> cB cB cA hE 9 0.0 0.00000 2
> cC cA cA hE 9 0.0 0.65103 3
> cC nN cA hE 9 0.0 0.00000 2
> cC oS cA hE 9 0.0 1.60373 3
> hA cA cA hE 9 0.0 0.65103 3
> hB cB cA hE 9 0.0 0.00000 2
> hE cA cA hE 9 0.0 0.65103 3
> hE cA cA hX 9 0.0 0.65103 3
> hE cA cA nA 9 0.0 0.65103 3
> hE cA cA nN 9 0.0 0.65084 3
> hE cA cA oH 9 0.0 0.00000 3
> hE cA cA oH 9 0.0 1.04600 1
> hE cA cA oS 9 0.0 0.00000 3
> hE cA cA oS 9 0.0 1.04600 1
> hE cA cA oT 9 0.0 0.00000 3
> hE cA cA oT 9 0.0 1.04600 1
> hE cA nN hN 9 0.0 0.00000 2
> hE cA oH hO 9 0.0 2.09200 3
> hE cA oT pA 9 0.0 1.60387 3
>
> Same thing for the ffnonbonded.itp:
> hE 1 1.008 0.0000 A 2,47135e-01 6,56888e-02
>
> And then we created a lipids.rtp file (here an example for a PC part of a
> lipid):
> [ PC ]
> [ atoms ]
> C11 cC 0.798859 1
> O12 oC -0.627537 2
> O11 oS -0.424905 3
> C1 cA -0.002091 4
> HR hE 0.119283 5
> HS hE 0.119283 6
> C2 cA 0.081076 7
> HX hE 0.131246 8
> C3 cA 0.095565 9
> HA hE 0.069089 10
> HB hE 0.069089 11
> O31 oZ -0.445682 12
> P31 pA 1.076564 13
> O32 oZ -0.445682 14
> C31 cA 0.363063 15
> H1A hE 0.013458 16
> H1B hE 0.013458 17
> C32 cA -0.282326 18
> H2A hX 0.164858 19
> H2B hX 0.164858 20
> N31 nA 0.198554 21
> C33 cA -0.395982 22
> H3A hX 0.194775 23
> H3B hX 0.194775 24
> H3C hX 0.194775 25
> C34 cA -0.395982 26
> H4A hX 0.194775 27
> H4B hX 0.194775 28
> H4C hX 0.194775 29
> C35 cA -0.395982 30
> H5A hX 0.194775 31
> H5B hX 0.194775 32
> H5C hX 0.194775 33
> O33 oP -0.793092 34
> O34 oP -0.793092 35
> O21 oS -0.390929 36
> C21 cC 0.787558 37
> O22 oC -0.625551 38
> [ bonds ]
> C11 O12
> C11 O11
> O11 C1
> C1 HR
> C1 HS
> C1 C2
> C2 HX
> C2 C3
> C2 O21
> C3 HA
> C3 HB
> C3 O31
> O31 P31
> P31 O32
> P31 033
> P31 034
> O32 C31
> C31 H1A
> C31 H1B
> C31 C32
> C32 H2A
> C32 H2B
> C32 N31
> N31 C33
> N31 C34
> N31 C35
> C33 H3A
> C33 H3B
> C33 H3C
> C34 H4A
> C34 H4B
> C34 H4C
> C35 H5A
> C35 H5B
> C35 H5C
> O21 C21
> C21 022
>
> Can you spot the mistake(s)?
>
> Thank you very much for your help in advance,
> Elisa
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