[gmx-users] Terminal dangling bond error despite pdb2gmx recognising specbond.dat for a cyclic peptide

[Alessandra Villa]

Hi,
I have just answered to your previous email. Please look at my answer.
Thank you
Alessandra

On Thu, Nov 28, 2019 at 9:41 AM Sahil Lall <slall at ncbs.res.in> wrote:

> Dear community,
>
> I want to use the OPLS-AA ff to understand the dynamics of a cyclic
> peptide with terminal-peptide-bonded Cystines that are also disulphide
> linked (i.e CxxxxxxC). To cyclise the N- and C- termini, I used a
> special bond in a specbond.dat file placed in my working directory.
>
> 2
> CYS N 1 CYS C 1 0.14 CYS CYS
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
>
> and after the pdb2gmx command I get the following response
>
> Identified residue CYS2 as a starting terminus.
> Identified residue CYS7 as a ending terminus.
> 2 out of 2 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                     CYS2    CYS2    CYS2    CYS7    CYS7
>                       N1      C3     SG6     N45     C47
>     CYS2      C3   0.244
>     CYS2     SG6   0.312   0.419
>     CYS7     N45   0.335   0.510   0.486
>     CYS7     C47   0.136   0.373   0.322   0.239
>     CYS7    SG50   0.387   0.482   0.205   0.420   0.365
> Linking CYS-2 N-1 and CYS-7 C-47...
> Linking CYS-2 SG-6 and CYS-7 SG-50...
>
> However, the problem arises with the -ter flag in the pdb2gmx command
>
> pdb2gmx -f in.pdb -o out.gro -ter -ignh
>
> The output is fine and links the terminal Cystines and putting a
> disulphide bond between them as shown above. But doesn't seem to be
> happy with the -ter command.
>
> Select start terminus type for CYS-2
> 0: NH3+
> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
> residue)
> 2: NH2
> 3: None
> 3
> Start terminus CYS-2: None
> Select end terminus type for CYS-7
> 0: COO-
> 1: ZWITTERION_COO- (only use with zwitterions containing exactly one
> residue)
> 2: COOH
> 3: None
> 3
> End terminus CYS-7: None
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.7
> Source code file:
> /home/ncbs/Downloads/gromacs-4.6.7/src/kernel/pdb2top.c, line: 1109
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your
> coordinate file, add a new terminal database entry (.tdb), or select the
> proper existing terminal entry.
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I cannot understand what is going wrong. The command only works if I
> choose NH2 as my N-terminus, however that in-principle violates the
> valence of the amide N and neutrality of the system.
>
> Thanks,
>
> Sahil
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