[gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic
Piggot T.
T.Piggot at soton.ac.uk
Thu Oct 26 12:01:23 CEST 2017
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
--
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.
More information about the gromacs.org_gmx-users
mailing list