[gmx-users] Re : Capping error in pdb2gmx

[Justin A. Lemkul]

On 6/10/12 3:14 PM, siddhant jain wrote:
> Thanks for mentioning my errors. I have corrected them. But now the problem is
> there is no rtp entry for NH2 in charmm. Here is what happens now-
>

If you want NH2 as a cap, you will need to come up with parameters for it.  An 
alternative is NAC.  See here:

http://lists.gromacs.org/pipermail/gmx-users/2010-July/052270.html

-Justin

> Using the Charmm27 force field in directory charmm27.ff
>
> pdb2gmx -f bestins.pdb -o first.gro -ter
>
> *entering 8 for charmm 27 force field*
>
> Opening force field file /usr/share/gromacs/top/charmm27.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP3P   TIP 3-point, recommended
>   2: TIP4P   TIP 4-point
>   3: TIPS3P  CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS)
>   4: SPC     simple point charge
>   5: SPC/E   extended simple point charge
>   6: None
> 1
> Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
> Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b
> Reading bestins.pdb...
> WARNING: all CONECT records are ignored
> Read 416 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> There are 2 chains and 0 blocks of water and 32 residues with 416 atoms
>
>    chain  #res #atoms
>    1 'A'    23    167
>    2 'B'    32    249
>
>
> WARNING: there were 1 atoms with zero occupancy and 15 atoms with
>           occupancy unequal to one (out of 416 atoms). Check your pdb file.
>
> Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (charmm27)
> Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
> Residue 43
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp
> Residue 47
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp
> Residue 59
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp
> Residue 63
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb
> Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.17#
> Processing chain 1 'A' (167 atoms, 23 residues)
> There are 31 donors and 35 acceptors
> There are 38 hydrogen bonds
> Identified residue ACE1 as a starting terminus.
> Identified residue NH223 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                      CYS7    CYS8   CYS12
>                      SG46    SG52    SG79
>      CYS8    SG52   0.691
>     CYS12    SG79   0.203   0.820
>     CYS21   SG157   1.140   1.613   1.215
> Linking CYS-7 SG-46 and CYS-12 SG-79...
> Select start terminus type for ACE-1
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus ACE-1: None
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581
>
> Fatal error:
> Residue 'NH2' 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
>
>
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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