[gmx-users] Capping of peptide terminal ends
Justin Lemkul
jalemkul at vt.edu
Sun Oct 14 14:12:23 CEST 2018
On 10/14/18 12:48 AM, Omkar Singh wrote:
> Hi ,
> I did same as you suggest me, but now new error is coming as shown below.
> I just backed up topol.top to ./#topol.top.30#
> Processing chain 1 (64 atoms, 7 residues)
> Identified residue ACE0 as a starting terminus.
> Identified residue CT31 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for ACE-0
> 0: NH3+
> 1: NH2
> 2: None
> 2
> Start terminus ACE-0: None
> Select end terminus type for CT3-1
> 0: CT3
> 1: COO-
> 2: COOH
> 3: CT2
> 4: None
> 4
> End terminus CT3-1: None
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.arn
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.arn
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.arn
>
> -------------------------------------------------------
> Program: gmx pdb2gmx, version 2016.2
> Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
>
> Fatal error:
> Atom H31 in residue ACE 0 was not found in rtp entry ACE with 6 atoms
> while sorting atoms.
>
> For a hydrogen, this can be a different protonation state, or it
> might have had a different number in the PDB file and was rebuilt
> (it might for instance have been H3, and we only expected H1 & H2).
> Note that hydrogens might have been added to the entry for the N-terminus.
> Remove this hydrogen or choose a different protonation state to solve it.
> Option -ignh will ignore all hydrogens in the input.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
If you follow this link, you will find the exact solution to your problem.
-Justin
> terminal entries are as following
> N-terminal
> ATOM 3 CH3 ACE 0 8.735 -0.604 2.523 1.00 0.00
> C
> ATOM 31 H31 ACE 0 9.608 0.044 2.605 1.00 0.00
> H
> ATOM 32 H32 ACE 0 8.348 -0.783 3.526 1.00 0.00
> H
> ATOM 33 H33 ACE 0 9.056 -1.553 2.095 1.00 0.00
> H
> ATOM 2 C ACE 1 7.677 0.041 1.642 1.00 0.00
> C
> ATOM 4 O ACE 1 7.890 1.122 1.099 1.00 0.00
> O
> ................................................................................................................
> C- terminal
>
> ATOM 23 N CT3 1 -5.561 0.819 -3.047 1.00 0.00
> N
> ATOM 50 HN CT3 1 -5.240 1.762 -2.900 1.00 0.00
> H
> ATOM 24 CH3 CT3 1 -6.804 0.635 -3.787 1.00 0.00
> C
> ATOM 51 H31 CT3 1 -7.250 1.599 -4.034 1.00 0.00
> H
> ATOM 52 H32 CT3 1 -6.624 0.095 -4.718 1.00 0.00
> H
> ATOM 53 H33 CT3 1 -7.527 0.065 -3.201 1.00 0.00
> H
> The spacing is fine in real pdb.
>
> On Fri, Oct 12, 2018 at 8:36 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/12/18 6:35 AM, Omkar Singh wrote:
>>> Hi all,
>>> I have a peptide system with capinng, N-ACE and C-NAC. i would like to
>>> create a topology file .I tried with pdb2gmx script but it is showing a
>>> fatal error like as;
>>> Fatal error:
>>> atom N not found in buiding block 1ACE while combining tdb and rtp. I
>>> already tried by editing in .rtp entry but after that it is showing
>> error.
>>> I am using CHARMM27 ff/
>>> Select the Force Field:
>>> From '/usr/local/gromacs/share/gromacs/top':
>>> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
>>> 1999-2012, 2003)
>>> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>>> 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res.
>> 29,
>>> 461-469, 1996)
>>> 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
>>> 1049-1074, 2000)
>>> 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
>>> 712-725, 2006)
>>> 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
>>> Proteins 78, 1950-58, 2010)
>>> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>>> 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>>> 9: CHARMM36 all-atom force field (March 2017)
>>> 10: GROMOS96 43a1 force field
>>> 11: GROMOS96 43a2 force field (improved alkane dihedrals)
>>> 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>>> 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>>> 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>>> 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856,
>> DOI:
>>> 10.1007/s00249-011-0700-9)
>>> 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>> 8
>>>
>>> Using the Charmm27 force field in directory charmm27.ff
>>>
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
>>> Reading a3k1.pdb...
>>> Read 'Structure1', 64 atoms
>>> Analyzing pdb file
>>> Splitting chemical chains based on TER records or chain id changing.
>>> There are 1 chains and 0 blocks of water and 6 residues with 64 atoms
>>>
>>> chain #res #atoms
>>> 1 ' ' 6 64
>>>
>>> All occupancies are one
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
>>> Atomtype 213
>>> Reading residue database... (charmm27)
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
>>> Residue 44
>>> Sorting it all out...
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
>>> Residue 48
>>> Sorting it all out...
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
>>> Residue 60
>>> Sorting it all out...
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
>>> Residue 64
>>> Sorting it all out...
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
>>> Opening force field file
>>> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb
>>>
>>> Back Off! I just backed up topol.top to ./#topol.top.8#
>>> Processing chain 1 (64 atoms, 6 residues)
>>> Identified residue ACE1 as a starting terminus.
>>> Identified residue CT35 as a ending terminus.
>>> 8 out of 8 lines of specbond.dat converted successfully
>>> Start terminus ACE-1: NH3+
>>> End terminus CT3-5: CT3
>> You need to specify "None" for both termini, otherwise pdb2gmx tries to
>> patch them as normal amino acids. The ACE and CT3 need to be present in
>> the input coordinate file as separate residues, appropriately named.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> 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.
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
More information about the gromacs.org_gmx-users
mailing list