Hi,
thank you for your answer.
I am using the last release version of AmberTools available on the
official website (AmberTools16)
I need parmed and openmm for computing the potential energy of a small
peptide (succeedly installed). While parmed alone allows me to load the
force fields parameters, computing the potential energy of a molecule
fails because the topology of the molecule is not loaded.
It seems that the only way is to load the topology from the prmtop file,
this is why I need to compile AmberTools, or at least the leap
executables for building such file.
Tom.
On 03/09/2017 02:33 PM, Daniel Roe wrote:
> Hi,
>
> Which version of AmberTools are you using?
>
> Also, if all you need is parmed you can always get it straight from
> GitHub: https://github.com/ParmEd/ParmEd
>
> -Dan
>
> On Thu, Mar 9, 2017 at 8:04 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
>>> Dear Amber developpers,
>>>
>>> We are very much interested in using the Amber force field. Of
>>> particular interest is the Python library Parmed
>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>> accessing the potential energy terms one by one.
>>>
>>> We need to generate the prmtop files, which requires the AmberTools suite.
>>>
>>> We have followed the steps described in the installation
>>> documentation, but unfortunately did not succeed to build the tools. I
>>> have got the following errors i am stuck with (see below).
>>>
>>> I am using Fedora 23 and try to compile using gcc.
>>>
>>> Can you please guide us on how to compile the tools ?
>>>
>>> Thank you for your attention.
>>>
>>> Tom.
>>>
>>> *In file included from pdb_type.cpp:29:**
>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>> error: conflicting types for 'memchr'**
>>> ** memchr(void* __s, int __c, size_t __n)**
>>> ** ^**
>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>> ** ^**
>>> **In file included from pdb_type.cpp:29:**
>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>> error: conflicting types for 'strchr'**
>>> ** strchr(char* __s, int __n)**
>>> ** ^**
>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>> **extern char *strchr (const char *__s, int __c)**
>>> ** ^**
>>> **In file included from pdb_type.cpp:29:**
>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>> error: conflicting types for 'strpbrk'**
>>> ** strpbrk(char* __s1, const char* __s2)**
>>> ** ^**
>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>> ** ^**
>>> **In file included from pdb_type.cpp:29:**
>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>> error: conflicting types for 'strrchr'**
>>> ** strrchr(char* __s, int __n)**
>>> ** ^**
>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>> **extern char *strrchr (const char *__s, int __c)**
>>> ** ^**
>>> **In file included from pdb_type.cpp:29:**
>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>> error: conflicting types for 'strstr'**
>>> ** strstr(char* __s1, const char* __s2)**
>>> ** ^**
>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>> ** ^**
>>> **5 errors generated.*
>>>
>>> AND
>>>
>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o CliqueList.o
>>> AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o -L../libpdb -lpdb++
>>> -L../toolclasses -ltoolclasses -lm **
>>> **/usr/bin/ld: cannot find -lpdb++**
>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>> invocation)**
>>> **Makefile:41: recipe for target 'reduce' failed*
>> On 03/09/2017 02:02 PM, Tom Dreyfus wrote:
>>>> Dear Amber developpers,
>>>>
>>>> We are very much interested in using the Amber force field. Of
>>>> particular interest is the Python library Parmed
>>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>>> accessing the potential energy terms one by one.
>>>>
>>>> We need to generate the prmtop files, which requires the AmberTools
>>>> suite.
>>>>
>>>> We have followed the steps described in the installation
>>>> documentation, but unfortunately did not succeed to build the tools.
>>>> I have got the following errors i am stuck with (see below).
>>>>
>>>> I am using Fedora 23 and try to compile using gcc.
>>>>
>>>> Can you please guide us on how to compile the tools ?
>>>>
>>>> Thank you for your attention.
>>>>
>>>> Tom.
>>>>
>>>> *In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>>> error: conflicting types for 'memchr'**
>>>> ** memchr(void* __s, int __c, size_t __n)**
>>>> ** ^**
>>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>>> error: conflicting types for 'strchr'**
>>>> ** strchr(char* __s, int __n)**
>>>> ** ^**
>>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>>> **extern char *strchr (const char *__s, int __c)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>>> error: conflicting types for 'strpbrk'**
>>>> ** strpbrk(char* __s1, const char* __s2)**
>>>> ** ^**
>>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>>> error: conflicting types for 'strrchr'**
>>>> ** strrchr(char* __s, int __n)**
>>>> ** ^**
>>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>>> **extern char *strrchr (const char *__s, int __c)**
>>>> ** ^**
>>>> **In file included from pdb_type.cpp:29:**
>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>>> error: conflicting types for 'strstr'**
>>>> ** strstr(char* __s1, const char* __s2)**
>>>> ** ^**
>>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>>> ** ^**
>>>> **5 errors generated.*
>>>>
>>>> AND
>>>>
>>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o
>>>> CliqueList.o AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o
>>>> -L../libpdb -lpdb++ -L../toolclasses -ltoolclasses -lm **
>>>> **/usr/bin/ld: cannot find -lpdb++**
>>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>>> invocation)**
>>>> **Makefile:41: recipe for target 'reduce' failed*
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>
>
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Received on Thu Mar 09 2017 - 06:00:04 PST
