AMBER Archive (2005)

Subject: RE: AMBER: xleap with modified residue

From: Whitney Allen (whitneygallen_at_yahoo.com)
Date: Mon Oct 24 2005 - 11:24:25 CDT

Whitney Allen <whitneygallen_at_yahoo.com> wrote:Hi Ross,
Thanks for the help. I applied the bug fixes and repeated all of the steps with the the residue name changed to TMG instead of 2MG. Unfortunately I still have the same problem. I have attached the pdb file and library file for you to look at.
 
Also, I have tried to create mol2 files instead of prepin files as suggested in a previous amber archive (http://structbio.vanderbilt.edu/archives/amber-archive/2004/0704.php), however, when I do this for my file (TMG.pdb) and the sustiva example found in tutorial 5 I can no longer used the "check", "edit", and "saveoff" commands needed to create a lib file (also seen in tutorial 4). Here are my commands and the error I get in xleap
 
source leaprc.gaff
loadmol2 sustiva.mol2
check SUS
check: Argument #1 is type String must be of type: [unit molecule resiude atom]
usage: check <unit> [parmset]
 
Thus it seems to me, that I can't just use mol2 instead of prepin. What can I do to fix this and used the more familiar mol2 format.
 
Thanks again for all of your help.
Whitney
 
 

Ross Walker <ross_at_rosswalker.co.uk> wrote:
Dear Whitney,
 
This sounds like it could be a bug with leap. Can you try repeating all the steps but this time call the unit MGG instead of 2MG. The number at the beginning of the unit name may be giving problems. Also replace the unit name mol with test. So
 
test = loadpdb test.pdb
 
Please make sure you have applied all the bugfixes from http://amber.scripps.edu/bugfixes80.html first since several of these deal with leap crashes.
 
If you still have problems please email me back with the library and pdb files and I'll see if I can reproduce the error.
 
All the best
Ross
 

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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---------------------------------
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Whitney Allen
Sent: Thursday, October 20, 2005 11:13
To: amber_at_scripps.edu
Subject: AMBER: xleap with modified residue

Hi Amber users

I am trying to run MD on a TRNA structure (6tna.pdb). This molecule has several modified bases and so I have used Antechamber to compute a molecule library for each modified base. However, after loading the library file into xleap (which is successful) I try and load the TRNA structure and xleap completely shuts down.

Below is the procedure that I follow. Note that I have tried to follow tutorials 4 & 5 as applicable. Here, for simplicity, I have cut the TRNA PDB file so that it contains only one modified residue (2MG or residue 10 in the 6tna.pdb file) and 15 total residues (residues 1-15 in the 6tna.pdb file) and have called it test.pdb. If anyone can help please reply and I can send you the 2MG.pdb, 2MG.mol2, 2mg.lib, and test.pdb files.

 

(Antechamber- note that I change the residue to a molecule)

 

% $AMBERHOME/exe/antechamber -i 2MG.pdb -fi pdb -o 2MG.mol2 -fo mol2 -c bcc -s 2 -mk "CARTESIAN AM1 STANDARD DIRECT OPT=LBFGS XTEST=0.0001"

 

% $AMBERHOME/exe/parmchk –i 2MG.mol2 –f mol2 –o 2MG.frcmod

 

% xleap –f leaprc.rna.ff99

source leaprc.gaff

loadmol2 2MG.mol2

check 2MG

edit 2MG

loadamberparms 2MG.frcmod

check 2MG

saveoff 2MG.lib

desc 2MG

 

 

% xleap –f leaprc.rna.ff99

source leaprc.gaff

loadoff 2mg.lib

check 2MG

mol=loadpdb test.pdb

 

(At this point xleap closes and I get the following error)

 

!FATAL ERROR----------------------------------------

!FATAL: In file [chirality.c], line 120

!FATAL: Message: Atom P is not in the first list

!

!ABORTING.

 

Please help me understand what is going on here and let me know how I can get this to work. It looks like all of the files are of normal format so I am a bit confused.

Thanks in advance

Whitney Hastings

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"TMG"
!entry.TMG.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"O1P" "o" 0 1 131072 1 8 -0.679350
"P" "p4" 0 1 131072 2 15 1.664610
"O2P" "o" 0 1 131072 3 8 -0.718480
"O5*" "os" 0 1 131072 4 8 -0.564450
"C5*" "c3" 0 1 131072 5 6 0.149810
"H51" "h1" 0 1 131072 6 1 0.069310
"H53" "h1" 0 1 131072 7 1 0.089570
"C4*" "c3" 0 1 131072 8 6 0.085200
"C3*" "c3" 0 1 131072 9 6 0.132190
"O3*" "oh" 0 1 131072 10 8 -0.574770
"H59" "ho" 0 1 131072 11 1 0.421450
"C2*" "c3" 0 1 131072 12 6 0.086950
"O2*" "oh" 0 1 131072 13 8 -0.595570
"H63" "ho" 0 1 131072 14 1 0.434280
"H61" "h1" 0 1 131072 15 1 0.090830
"H57" "h1" 0 1 131072 16 1 0.118460
"H55" "h1" 0 1 131072 17 1 0.090000
"O4*" "os" 0 1 131072 18 8 -0.421730
"C1*" "c3" 0 1 131072 19 6 0.224060
"H65" "h2" 0 1 131072 20 1 0.096220
"N9" "na" 0 1 131072 21 7 -0.232040
"C4" "cc" 0 1 131072 22 6 0.107960
"N3" "nc" 0 1 131072 23 7 -0.699550
"C8" "cc" 0 1 131072 24 6 0.392550
"H67" "h5" 0 1 131072 25 1 0.085790
"N7" "nd" 0 1 131072 26 7 -0.579410
"C5" "cd" 0 1 131072 27 6 0.181980
"C6" "c" 0 1 131072 28 6 0.652640
"O6" "o" 0 1 131072 29 8 -0.587650
"N1" "n" 0 1 131072 30 7 -0.511320
"H69" "hn" 0 1 131072 31 1 0.335970
"C2" "cd" 0 1 131072 32 6 0.698490
"N2" "nh" 0 1 131072 33 7 -0.805780
"H71" "hn" 0 1 131072 34 1 0.419310
"C2A" "c3" 0 1 131072 35 6 0.188750
"H73" "h1" 0 1 131072 36 1 0.055130
"H75" "h1" 0 1 131072 37 1 0.031960
"H77" "h1" 0 1 131072 38 1 0.066620
!entry.TMG.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"O1P" "o" 0 -1 0.0
"P" "p4" 0 -1 0.0
"O2P" "o" 0 -1 0.0
"O5*" "os" 0 -1 0.0
"C5*" "c3" 0 -1 0.0
"H51" "h1" 0 -1 0.0
"H53" "h1" 0 -1 0.0
"C4*" "c3" 0 -1 0.0
"C3*" "c3" 0 -1 0.0
"O3*" "oh" 0 -1 0.0
"H59" "ho" 0 -1 0.0
"C2*" "c3" 0 -1 0.0
"O2*" "oh" 0 -1 0.0
"H63" "ho" 0 -1 0.0
"H61" "h1" 0 -1 0.0
"H57" "h1" 0 -1 0.0
"H55" "h1" 0 -1 0.0
"O4*" "os" 0 -1 0.0
"C1*" "c3" 0 -1 0.0
"H65" "h2" 0 -1 0.0
"N9" "na" 0 -1 0.0
"C4" "cc" 0 -1 0.0
"N3" "nc" 0 -1 0.0
"C8" "cc" 0 -1 0.0
"H67" "h5" 0 -1 0.0
"N7" "nd" 0 -1 0.0
"C5" "cd" 0 -1 0.0
"C6" "c" 0 -1 0.0
"O6" "o" 0 -1 0.0
"N1" "n" 0 -1 0.0
"H69" "hn" 0 -1 0.0
"C2" "cd" 0 -1 0.0
"N2" "nh" 0 -1 0.0
"H71" "hn" 0 -1 0.0
"C2A" "c3" 0 -1 0.0
"H73" "h1" 0 -1 0.0
"H75" "h1" 0 -1 0.0
"H77" "h1" 0 -1 0.0
!entry.TMG.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.TMG.unit.childsequence single int
2
!entry.TMG.unit.connect array int
1
35
!entry.TMG.unit.connectivity table int atom1x int atom2x int flags
1 2 1
2 3 1
2 4 1
4 5 1
5 6 1
5 7 1
5 8 1
8 9 1
8 17 1
8 18 1
9 10 1
9 12 1
9 16 1
10 11 1
12 13 1
12 15 1
12 19 1
13 14 1
18 19 1
19 20 1
19 21 1
21 22 1
21 24 1
22 23 1
22 27 1
23 32 1
24 25 1
24 26 1
26 27 1
27 28 1
28 29 1
28 30 1
30 31 1
30 32 1
32 33 1
33 34 1
33 35 1
35 36 1
35 37 1
35 38 1
!entry.TMG.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
"R" 1 "A" 18
"R" 1 "A" 19
"R" 1 "A" 20
"R" 1 "A" 21
"R" 1 "A" 22
"R" 1 "A" 23
"R" 1 "A" 24
"R" 1 "A" 25
"R" 1 "A" 26
"R" 1 "A" 27
"R" 1 "A" 28
"R" 1 "A" 29
"R" 1 "A" 30
"R" 1 "A" 31
"R" 1 "A" 32
"R" 1 "A" 33
"R" 1 "A" 34
"R" 1 "A" 35
"R" 1 "A" 36
"R" 1 "A" 37
"R" 1 "A" 38
!entry.TMG.unit.name single str
"TMG"
!entry.TMG.unit.positions table dbl x dbl y dbl z
3.536914 1.422858 -1.933042E-06
2.624412 1.239175 -1.155795
2.724479 2.272550 -2.218959
1.119680 1.136345 -0.630803
0.289627 2.313553 -0.745771
0.498511 2.942111 0.003418
0.470806 2.764012 -1.619991
-1.184781 1.910741 -0.676749
-1.473194 0.556363 -0.054815
-1.695417 0.649988 1.346590
-1.881662 -0.260203 1.716544
-2.698993 0.099201 -0.832571
-3.869334 0.739085 -0.345488
-4.662899 0.426537 -0.867570
-2.840084 -0.889727 -0.786586
-0.713919 -0.091251 -0.118820
-1.616013 2.581909 -0.073779
-1.721816 1.911745 -2.025785
-2.423311 0.683776 -2.223726
-3.299598 0.798135 -2.691748
-1.598749 -0.192597 -3.083672
-2.004608 -1.393650 -3.643801
-3.235802 -1.950071 -3.471752
-0.297764 -0.023102 -3.514800
0.258871 0.769132 -3.264755
0.143096 -0.991350 -4.280868
-0.939499 -1.868608 -4.365856
-1.060220 -3.100214 -5.054063
-0.228353 -3.683494 -5.750918
-2.332763 -3.664457 -4.871084
-2.519130 -4.539864 -5.317100
-3.350781 -3.098405 -4.118095
-4.484665 -3.801677 -4.074056
-4.591993 -4.674626 -4.549914
-5.564085 -3.201554 -3.276807
-6.367821 -3.795974 -3.302774
-5.799737 -2.306201 -3.654709
-5.260363 -3.094025 -2.330133
!entry.TMG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 35 0 0 0 0
!entry.TMG.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"TMG" 1 39 1 "?" 0
!entry.TMG.unit.residuesPdbSequenceNumber array int
0
!entry.TMG.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.TMG.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0

                
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